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Ji L, Zhang H, Ding W, Song R, Han Y, Yu H, Paneth P. Theoretical Kinetic Isotope Effects in Establishing the Precise Biodegradation Mechanisms of Organic Pollutants. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:4915-4929. [PMID: 36926881 DOI: 10.1021/acs.est.2c04755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Compound-specific isotope analysis (CSIA) for natural isotope ratios has been recognized as a promising tool to elucidate biodegradation pathways of organic pollutants by microbial enzymes by relating reported kinetic isotope effects (KIEs) to apparent KIEs (AKIEs) derived from bulk isotope fractionations (εbulk). However, for many environmental reactions, neither are the reference KIE ranges sufficiently narrow nor are the mechanisms elucidated to the point that rate-determining steps have been identified unequivocally. In this work, besides providing reference KIEs and rationalizing AKIEs, good relationships have been explained by DFT computations for diverse biodegradation pathways with known enzymatic models between the theoretical isotope fractionations (εbulk') from intrinsic KIEs on the rate-determining steps and the observed εbulk. (1) To confirm the mechanistic details of previously reported pathway-dependent CSIA, it includes isotope changes in MTBE biodegradation between hydroxylation by CYP450 and SN2 reaction by cobalamin-dependent methyltransferase, the regioselectivity of toluene biodegradation by CYP450, and the rate-determining step in toluene biodegradation by benzylsuccinate synthase. (2) To yield new fundamental insights into some unclear biodegradation pathways, it consists of the oxidative function of toluene dioxygenase in biodegradation of TCE, the epoxidation mode in biodegradation of TCE by toluene 4-monooxygenase, and the weighted average mechanism in biodegradation of cDCE by CYP450.
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Affiliation(s)
- Li Ji
- School of Environment Science and Spatial Informatics, China University of Mining and Technology, Daxue Road 1, Xuzhou 221116, China
| | - Huanni Zhang
- School of Environment Science and Spatial Informatics, China University of Mining and Technology, Daxue Road 1, Xuzhou 221116, China
- College of Environmental and Resource Sciences, Zhejiang University, Yuhangtang Road 866, Hangzhou 310058, China
| | - Wen Ding
- School of Environment Science and Spatial Informatics, China University of Mining and Technology, Daxue Road 1, Xuzhou 221116, China
| | - Runqian Song
- School of Environment Science and Spatial Informatics, China University of Mining and Technology, Daxue Road 1, Xuzhou 221116, China
- College of Environmental and Resource Sciences, Zhejiang University, Yuhangtang Road 866, Hangzhou 310058, China
| | - Ye Han
- School of Environment Science and Spatial Informatics, China University of Mining and Technology, Daxue Road 1, Xuzhou 221116, China
| | - Haiying Yu
- College of Geography and Environmental Sciences, Zhejiang Normal University, Jinhua 321004, China
| | - Piotr Paneth
- Institute of Applied Radiation Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego 116, Lodz 90-924, Poland
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2
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Bennett CS. Glycosyl Sulfonates Beyond Triflates. CHEM REC 2021; 21:3102-3111. [PMID: 34142755 PMCID: PMC10923190 DOI: 10.1002/tcr.202100141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Revised: 06/03/2021] [Indexed: 11/10/2022]
Abstract
While glycosyl triflates are frequently invoked as intermediates in many chemical glycosylation reactions, the chemistry of other glycosyl sulfonates remains comparatively underexplored. Given the reactivity of sulfonates can span several orders of magnitude, this represents an untapped resource for the development of stereoselective glycosylation reactions. This personal account describes our laboratories efforts to take advantage of this reactivity to develop β-specific glycosylation reactions. Initial investigations led to the development of 2-deoxy-sugar tosylates as highly selective donors for β-glycoside synthesis, an approach which has been used to great success by our group and others for the construction of deoxy-sugar oligosaccharides and natural products. Subsequent studies demonstrate that "matching" the reactivity of the sulfonate to that of the sugar donor leads to highly selective SN 2-glycosylations with a range of substrates.
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Affiliation(s)
- Clay S Bennett
- Department of Chemistry, Tufts University, 62 Talbot Ave., 02155, Medford, MA, USA
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3
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Farren-Dai M, Sannikova N, Świderek K, Moliner V, Bennet AJ. Fundamental Insight into Glycoside Hydrolase-Catalyzed Hydrolysis of the Universal Koshland Substrates–Glycopyranosyl Fluorides. ACS Catal 2021. [DOI: 10.1021/acscatal.1c01918] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Marco Farren-Dai
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Natalia Sannikova
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Katarzyna Świderek
- Biocomp Group, Institute of Advanced Materials (INAM), Universitat Jaume I, Castellón 12071, Spain
| | - Vicent Moliner
- Biocomp Group, Institute of Advanced Materials (INAM), Universitat Jaume I, Castellón 12071, Spain
| | - Andrew J. Bennet
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
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4
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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: 6] [Impact Index Per Article: 2.0] [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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5
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Takeuchi H, Fujimori Y, Ueda Y, Shibayama H, Nagaishi M, Yoshimura T, Sasamori T, Tokitoh N, Furuta T, Kawabata T. Solvent-Dependent Mechanism and Stereochemistry of Mitsunobu Glycosylation with Unprotected Pyranoses. Org Lett 2020; 22:4754-4759. [DOI: 10.1021/acs.orglett.0c01549] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Hironori Takeuchi
- Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan
| | - Yusuke Fujimori
- Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan
| | - Yoshihiro Ueda
- Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan
| | - Hiromitsu Shibayama
- Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan
| | - Masaru Nagaishi
- Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan
| | - Tomoyuki Yoshimura
- Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan
| | - Takahiro Sasamori
- Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan
| | - Norihiro Tokitoh
- Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan
| | - Takumi Furuta
- Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan
| | - Takeo Kawabata
- Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan
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6
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Takahashi D. Development and Application of Boronic-Acid-Catalyzed Regioselective and 1,2-cis-Stereoselective Glycosylation. J SYN ORG CHEM JPN 2020. [DOI: 10.5059/yukigoseikyokaishi.78.221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Daisuke Takahashi
- Department of Applied Chemistry, Faculty of Science and Technology, Keio University
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7
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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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8
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Barrios Antúnez DJ, Greenhalgh MD, Brueckner AC, Walden DM, Elías-Rodríguez P, Roberts P, Young BG, West TH, Slawin AMZ, Ha-Yeon Cheong P, Smith AD. Catalytic enantioselective synthesis of perfluoroalkyl-substituted β-lactones via a concerted asynchronous [2 + 2] cycloaddition: a synthetic and computational study. Chem Sci 2019; 10:6162-6173. [PMID: 31360423 PMCID: PMC6585878 DOI: 10.1039/c9sc00390h] [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] [Received: 01/23/2019] [Accepted: 04/27/2019] [Indexed: 11/21/2022] Open
Abstract
The enantioselective preparation of a range of perfluoroalkyl-substituted β-lactones through an isothiourea (HyperBTM) catalysed reaction using symmetric anhydrides as ammonium enolate precursors and perfluoroalkylketones (RF = CF3, C2F5, C4F9) is reported. Following optimisation, high diastereo- and enantioselectivity was observed for β-lactone formation using C2F5- and C4F9-substituted ketones at room temperature (26 examples, up to >95 : 5 dr and >99 : 1 er), whilst -78 °C was necessary for optimal dr and er with CF3-substituted ketones (11 examples, up to >95 : 5 dr and >99 : 1 er). Derivatisation of the β-lactones through ring-opening, as well as a two-step conversion to give perfluoroalkyl-substituted oxetanes, is demonstrated without loss of stereochemical integrity. Density functional theory computations, alongside 13C natural abundance KIE studies, have been used to probe the reaction mechanism with a concerted asynchronous [2 + 2]-cycloaddition pathway favoured over a stepwise aldol-lactonisation process.
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Affiliation(s)
| | - Mark D Greenhalgh
- EaStCHEM , School of Chemistry , University of St Andrews , North Haugh , St Andrews , KY16 9ST , UK .
| | - Alexander C Brueckner
- Department of Chemistry , Oregon State University , 153 Gilbert Hall , Corvallis , Oregon 97333 , USA .
| | - Daniel M Walden
- Department of Chemistry , Oregon State University , 153 Gilbert Hall , Corvallis , Oregon 97333 , USA .
| | - Pilar Elías-Rodríguez
- EaStCHEM , School of Chemistry , University of St Andrews , North Haugh , St Andrews , KY16 9ST , UK .
| | - Patrick Roberts
- EaStCHEM , School of Chemistry , University of St Andrews , North Haugh , St Andrews , KY16 9ST , UK .
| | - Benjamin G Young
- Department of Chemistry, Physics, and Engineering , Biola University , 315 Lim Center , La Mirada , California 90639 , USA
| | - Thomas H West
- EaStCHEM , School of Chemistry , University of St Andrews , North Haugh , St Andrews , KY16 9ST , UK .
| | - Alexandra M Z Slawin
- EaStCHEM , School of Chemistry , University of St Andrews , North Haugh , St Andrews , KY16 9ST , UK .
| | - Paul Ha-Yeon Cheong
- Department of Chemistry , Oregon State University , 153 Gilbert Hall , Corvallis , Oregon 97333 , USA .
| | - Andrew D Smith
- EaStCHEM , School of Chemistry , University of St Andrews , North Haugh , St Andrews , KY16 9ST , UK .
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9
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Adero PO, Amarasekara H, Wen P, Bohé L, Crich D. The Experimental Evidence in Support of Glycosylation Mechanisms at the S N1-S N2 Interface. Chem Rev 2018; 118:8242-8284. [PMID: 29846062 PMCID: PMC6135681 DOI: 10.1021/acs.chemrev.8b00083] [Citation(s) in RCA: 215] [Impact Index Per Article: 35.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A critical review of the state-of-the-art evidence in support of the mechanisms of glycosylation reactions is provided. Factors affecting the stability of putative oxocarbenium ions as intermediates at the SN1 end of the mechanistic continuum are first surveyed before the evidence, spectroscopic and indirect, for the existence of such species on the time scale of glycosylation reactions is presented. Current models for diastereoselectivity in nucleophilic attack on oxocarbenium ions are then described. Evidence in support of the intermediacy of activated covalent glycosyl donors is reviewed, before the influences of the structure of the nucleophile, of the solvent, of temperature, and of donor-acceptor hydrogen bonding on the mechanism of glycosylation reactions are surveyed. Studies on the kinetics of glycosylation reactions and the use of kinetic isotope effects for the determination of transition-state structure are presented, before computational models are finally surveyed. The review concludes with a critical appraisal of the state of the art.
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Affiliation(s)
- Philip Ouma Adero
- Department of Chemistry , Wayne State University , 5101 Cass Avenue , Detroit , Michigan 48202 , United States
| | - Harsha Amarasekara
- Department of Chemistry , Wayne State University , 5101 Cass Avenue , Detroit , Michigan 48202 , United States
| | - Peng Wen
- Department of Chemistry , Wayne State University , 5101 Cass Avenue , Detroit , Michigan 48202 , United States
| | - Luis Bohé
- Institut de Chimie des Substances Naturelles, CNRS UPR 2301 , Université Paris-Sud Université Paris-Saclay , 1 avenue de la Terrasse , 91198 Gif-sur-Yvette , France
| | - David Crich
- Department of Chemistry , Wayne State University , 5101 Cass Avenue , Detroit , Michigan 48202 , United States
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10
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Tanaka M, Nakagawa A, Nishi N, Iijima K, Sawa R, Takahashi D, Toshima K. Boronic-Acid-Catalyzed Regioselective and 1,2- cis-Stereoselective Glycosylation of Unprotected Sugar Acceptors via S Ni-Type Mechanism. J Am Chem Soc 2018; 140:3644-3651. [PMID: 29457892 DOI: 10.1021/jacs.7b12108] [Citation(s) in RCA: 79] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Regio- and 1,2- cis-stereoselective chemical glycosylation of unprotected glycosyl acceptors has been in great demand for the efficient synthesis of natural glycosides. However, simultaneously regulating these selectivities has been a longstanding problem in synthetic organic chemistry. In nature, glycosyl transferases catalyze regioselective 1,2- cis-glycosylations via the SNi mechanism, yet no useful chemical glycosylations based on this mechanism have been developed. In this paper, we report a highly regio- and 1,2- cis-stereoselective SNi-type glycosylation of 1,2-anhydro donors and unprotected sugar acceptors using p-nitrophenylboronic acid (10e) as a catalyst in the presence of water under mild conditions. Highly controlled regio- and 1,2- cis-stereoselectivities were achieved via the combination of boron-mediated carbohydrate recognition and the SNi-type mechanism. Mechanistic studies using the KIEs and DFT calculations were consistent with a highly dissociative concerted SNi mechanism. This glycosylation method was applied successfully to the direct glycosylation of unprotected natural glycosides and the efficient synthesis of a complex oligosaccharide with minimal protecting groups.
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Affiliation(s)
- Masamichi Tanaka
- Department of Applied Chemistry, Faculty of Science and Technology , Keio University , 3-14-1 Hiyoshi , Kohoku-ku, Yokohama 223-8522 , Japan
| | - Akira Nakagawa
- Department of Applied Chemistry, Faculty of Science and Technology , Keio University , 3-14-1 Hiyoshi , Kohoku-ku, Yokohama 223-8522 , Japan
| | - Nobuya Nishi
- Department of Applied Chemistry, Faculty of Science and Technology , Keio University , 3-14-1 Hiyoshi , Kohoku-ku, Yokohama 223-8522 , Japan
| | - Kiyoko Iijima
- Institute of Microbial Chemistry (BIKAKEN) , 3-14-23 Kamiosaki , Shinagawa-ku, Tokyo 141-0021 , Japan
| | - Ryuichi Sawa
- Institute of Microbial Chemistry (BIKAKEN) , 3-14-23 Kamiosaki , Shinagawa-ku, Tokyo 141-0021 , Japan
| | - Daisuke Takahashi
- Department of Applied Chemistry, Faculty of Science and Technology , Keio University , 3-14-1 Hiyoshi , Kohoku-ku, Yokohama 223-8522 , Japan
| | - Kazunobu Toshima
- Department of Applied Chemistry, Faculty of Science and Technology , Keio University , 3-14-1 Hiyoshi , Kohoku-ku, Yokohama 223-8522 , Japan
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11
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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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12
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Montgomery AP, Xiao K, Wang X, Skropeta D, Yu H. Computational Glycobiology: Mechanistic Studies of Carbohydrate-Active Enzymes and Implication for Inhibitor Design. STRUCTURAL AND MECHANISTIC ENZYMOLOGY 2017; 109:25-76. [DOI: 10.1016/bs.apcsb.2017.04.003] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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13
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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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14
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Speciale G, Farren-Dai M, Shidmoossavee FS, Williams SJ, Bennet AJ. C2-Oxyanion Neighboring Group Participation: Transition State Structure for the Hydroxide-Promoted Hydrolysis of 4-Nitrophenyl α-d-Mannopyranoside. J Am Chem Soc 2016; 138:14012-14019. [DOI: 10.1021/jacs.6b07935] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Gaetano Speciale
- School
of Chemistry and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, 30 Flemington Road, Parkville, Victoria 3010, Australia
| | - Marco Farren-Dai
- Department
of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, B.C. V5A 1S6, Canada
| | - Fahimeh S. Shidmoossavee
- Department
of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, B.C. V5A 1S6, Canada
| | - Spencer J. Williams
- School
of Chemistry and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, 30 Flemington Road, Parkville, Victoria 3010, Australia
| | - Andrew J. Bennet
- Department
of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, B.C. V5A 1S6, Canada
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15
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Chan J, Tang A, Bennet AJ. Transition-state structure for the hydronium-ion-promoted hydrolysis of α-d-glucopyranosyl fluoride. CAN J CHEM 2015. [DOI: 10.1139/cjc-2014-0451] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The transition state for the hydronium-ion-promoted hydrolysis of α-d-glucopyranosyl fluoride in water has been characterized by combining multiple kinetic isotope effect measurements with theoretical modelling. The measured kinetic isotope effects for the C1-deuterium, C2-deuterium, C5-deuterium, anomeric carbon-13, and ring oxygen-18 are 1.219 ± 0.021, 1.099 ± 0.024, 0.976 ± 0.014, 1.014 ± 0.005, and 0.991 ± 0.013, respectively. The transition state for the hydronium ion reaction is late with respect to both C–F bond cleavage and proton transfer.
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Affiliation(s)
- Jefferson Chan
- Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC V5A 1S6, Canada
- Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC V5A 1S6, Canada
| | - Ariel Tang
- Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC V5A 1S6, Canada
- Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC V5A 1S6, Canada
| | - Andrew J. Bennet
- Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC V5A 1S6, Canada
- Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC V5A 1S6, Canada
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16
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Xie M, Byers LD. Solvent and α-secondary kinetic isotope effects on β-glucosidase. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1854:1776-81. [PMID: 25770682 DOI: 10.1016/j.bbapap.2015.02.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2015] [Accepted: 02/23/2015] [Indexed: 11/20/2022]
Abstract
β-Glucosidase from sweet almond is a retaining, family 1, glycohydrolase. It is known that glycosylation of the enzyme by aryl glucosides occurs with little, if any, acid catalysis. For this reaction both the solvent and α-secondary kinetic isotope effects are 1.0. However, for the deglucosylation reaction (e.g., kcat for 2,4-dinitrophenyl-β-D-glucopyranoside) there is a small solvent deuterium isotope effect of 1.50 (±0.06) and an α-secondary kinetic isotope effect of 1.12 (±0.03). For aryl glucosides, kcat/KM is very sensitive to the pKa of the phenol leaving group [βlg≈-1; Dale et al., Biochemistry25 (1986) 2522-2529]. With alkyl glucosides the βlg is smaller (between -0.2 and -0.3) but still negative. This, coupled with the small solvent isotope effect on the pH-independent second-order rate constant for the glucosylation of the enzyme with 2,2,2-trifluoroethyl-β-glucoside [D2O(kcat/KM)=1.23 (±0.04)] suggests that there is more glycone-aglycone bond fission than aglycone oxygen protonation in the transition state for alkyl glycoside hydrolysis. The kinetics constants for the partitioning (between water and various alcohols) of the glucosyl-enzyme intermediate, coupled with the rate constants for the forward (hydrolysis) reaction provide an estimate of the stability of the glucosyl-enzyme intermediate. This is a relatively stable species with an energy about 2 to 4 kcal/mol higher than that of the ES complex. This article is part of a Special Issue entitled: Enzyme Transition States from Theory and Experiment.
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Affiliation(s)
- Miaomiao Xie
- Department of Chemistry, Tulane University, New Orleans, LA 70118, USA
| | - Larry D Byers
- Department of Chemistry, Tulane University, New Orleans, LA 70118, USA.
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17
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Cheng GJ, Zhang X, Chung LW, Xu L, Wu YD. Computational organic chemistry: bridging theory and experiment in establishing the mechanisms of chemical reactions. J Am Chem Soc 2015; 137:1706-25. [PMID: 25568962 DOI: 10.1021/ja5112749] [Citation(s) in RCA: 234] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Understanding the mechanisms of chemical reactions, especially catalysis, has been an important and active area of computational organic chemistry, and close collaborations between experimentalists and theorists represent a growing trend. This Perspective provides examples of such productive collaborations. The understanding of various reaction mechanisms and the insight gained from these studies are emphasized. The applications of various experimental techniques in elucidation of reaction details as well as the development of various computational techniques to meet the demand of emerging synthetic methods, e.g., C-H activation, organocatalysis, and single electron transfer, are presented along with some conventional developments of mechanistic aspects. Examples of applications are selected to demonstrate the advantages and limitations of these techniques. Some challenges in the mechanistic studies and predictions of reactions are also analyzed.
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Affiliation(s)
- Gui-Juan Cheng
- Lab of Computational Chemistry and Drug Design, Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School , Shenzhen 518055, China
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18
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Chakladar S, Wang Y, Clark T, Cheng L, Ko S, Vocadlo DJ, Bennet AJ. A mechanism-based inactivator of glycoside hydrolases involving formation of a transient non-classical carbocation. Nat Commun 2014; 5:5590. [DOI: 10.1038/ncomms6590] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2014] [Accepted: 10/16/2014] [Indexed: 12/21/2022] Open
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19
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Chan J, Sannikova N, Tang A, Bennet AJ. Transition-State Structure for the Quintessential SN2 Reaction of a Carbohydrate: Reaction of α-Glucopyranosyl Fluoride with Azide Ion in Water. J Am Chem Soc 2014; 136:12225-8. [DOI: 10.1021/ja506092h] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Jefferson Chan
- Chemistry Department, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada
| | - Natalia Sannikova
- Chemistry Department, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada
| | - Ariel Tang
- Chemistry Department, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada
| | - Andrew J. Bennet
- Chemistry Department, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada
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20
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Xiang S, Meyer MP. A general approach to mechanism in multiproduct reactions: product-specific intermolecular kinetic isotope effects. J Am Chem Soc 2014; 136:5832-5. [PMID: 24721128 DOI: 10.1021/ja412827c] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Here we report a general method for the measurement of (13)C kinetic isotope effects at natural abundance for reactions that yield two or more products concurrently. We use, as an example, a recently reported Co-catalyzed reaction between cyclopentene and 1-phenyl-1-propyne. High-precision intermolecular (13)C isotope effects are reported for both the formal [2+2] cycloaddition (major) and Alder-ene (minor) reaction products. Mechanistic possibilities that are in accord with observed isotope effect measurements are discussed.
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Affiliation(s)
- Shuhuai Xiang
- Department of Chemistry and Biochemistry, University of California , Merced, California 95343, United States
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21
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Advances in kinetic isotope effect measurement techniques for enzyme mechanism study. Molecules 2013; 18:9278-92. [PMID: 23917115 PMCID: PMC6270257 DOI: 10.3390/molecules18089278] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2013] [Revised: 07/22/2013] [Accepted: 07/29/2013] [Indexed: 11/17/2022] Open
Abstract
Kinetic isotope effects (KIEs) are a very powerful tool for investigating enzyme mechanisms. Precision of measurement is the most important factor for KIE determinations, especially for small heavy atom KIEs. Internal competition is commonly used to measure small KIEs on V/K. Several methods, including such as liquid scintillation counting, mass spectrometry, nuclear magnetic resonance spectroscopy and polarimetry have been used to determine KIEs. In this paper, which does not aspire to be an exhaustive review, we briefly review different experimental approaches for the measurement of KIEs on enzymatic reaction with an emphasis on newer techniques employing mass spectrometry and nuclear magnetic resonance spectrometry as well as some corresponding examples.
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22
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Manning KA, Sathyamoorthy B, Eletsky A, Szyperski T, Murkin AS. Highly precise measurement of kinetic isotope effects using 1H-detected 2D [13C,1H]-HSQC NMR spectroscopy. J Am Chem Soc 2012; 134:20589-92. [PMID: 23215000 DOI: 10.1021/ja310353c] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A new method is presented for measuring kinetic isotope effects (KIEs) by (1)H-detected 2D [(13)C,(1)H]-heteronuclear single quantum coherence (HSQC) NMR spectroscopy. The high accuracy of this approach was exemplified for the reaction catalyzed by glucose-6-phosphate dehydrogenase by comparing the 1-(13)C KIE with the published value obtained using isotope ratio mass spectrometry. High precision was demonstrated for the reaction catalyzed by 1-deoxy-D-xylulose-5-phosphate reductoisomerase from Mycobacterium tuberculosis. 2-, 3-, and 4-(13)C KIEs were found to be 1.0031(4), 1.0303(12), and 1.0148(2), respectively. These KIEs provide evidence for a cleanly rate-limiting retroaldol step during isomerization. The high intrinsic sensitivity and signal dispersion of 2D [(13)C,(1)H]-HSQC offer new avenues to study challenging systems where low substrate concentration and/or signal overlap impedes 1D (13)C NMR data acquisition. Moreover, this approach can take advantage of highest-field spectrometers, which are commonly equipped for (1)H detection with cryogenic probes.
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Affiliation(s)
- Kathryn A Manning
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, New York 14260-3000, USA
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23
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Kinetic isotope effects for studying post-translational modifying enzymes. Curr Opin Chem Biol 2012; 16:472-8. [PMID: 23146439 DOI: 10.1016/j.cbpa.2012.10.024] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2012] [Revised: 10/14/2012] [Accepted: 10/15/2012] [Indexed: 11/20/2022]
Abstract
The ongoing development of new experimental approaches for the measurement of isotope effects is improving our understanding of the physical and chemical changes that occur during biological catalysis. Biological catalysis involves numerous steps that include binding, conformational changes, chemical catalysis and product release. The critical points on the free energy surface for biologically catalyzed reactions include all bound intermediates and the intervening transition states. Isotope effects can be used to investigate both intermediate (equilibrium isotope effects) and transition state (kinetic isotope effects) structures along the reaction coordinate. This review details new techniques for measuring isotope effects and provides several examples of their use in solving transition state structures for post-translational modifying enzymes.
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24
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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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25
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Huang M, Garrett GE, Birlirakis N, Bohé L, Pratt DA, Crich D. Dissecting the mechanisms of a class of chemical glycosylation using primary ¹³C kinetic isotope effects. Nat Chem 2012; 4:663-7. [PMID: 22824899 PMCID: PMC3404748 DOI: 10.1038/nchem.1404] [Citation(s) in RCA: 153] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2011] [Accepted: 06/07/2012] [Indexed: 01/13/2023]
Abstract
Although arguably the most important reaction in glycoscience, chemical glycosylations are among the least well understood of organic chemical reactions, resulting in an unnecessarily high degree of empiricism and a brake on rational development in this critical area. To address this problem, primary (13)C kinetic isotope effects have now been determined for the formation of β- and α-manno- and glucopyranosides using a natural abundance NMR method. In contrast to the common current assumption, for three of the four cases studied the experimental and computed values are indicative of associative displacement of the intermediate covalent glycosyl trifluoromethanesulfonates. For the formation of the α-mannopyranosides, the experimentally determined KIE differs significantly from that computed for an associative displacement, which is strongly suggestive of a dissociative mechanism that approaches the intermediacy of a glycosyl oxocarbenium ion. The application of analogous experiments to other glycosylation systems should shed further light on their mechanisms and thus assist in the design of better reactions conditions with improved stereoselectivity.
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Affiliation(s)
- Min Huang
- Centre de Recherche de Gif, Institut de Chimie des Substances Naturelles, CNRS, Avenue de Terrasse, 91198 Gif-sur-Yvette, France
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26
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Chan J, Lewis AR, Indurugalla D, Schur M, Wakarchuk W, Bennet AJ. Transition State Analysis of Vibrio cholerae Sialidase-Catalyzed Hydrolyses of Natural Substrate Analogues. J Am Chem Soc 2012; 134:3748-57. [DOI: 10.1021/ja208564y] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Jefferson Chan
- Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby,
British Columbia, V5A 1S6, Canada
| | - Andrew R. Lewis
- Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby,
British Columbia, V5A 1S6, Canada
| | - Deepani Indurugalla
- Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby,
British Columbia, V5A 1S6, Canada
| | - Melissa Schur
- Institute for Biological Sciences, National Research Council Canada, Ottawa, Ontario,
Canada
| | - Warren Wakarchuk
- Institute for Biological Sciences, National Research Council Canada, Ottawa, Ontario,
Canada
| | - Andrew J. Bennet
- Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby,
British Columbia, V5A 1S6, Canada
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27
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Meyer MP. New Applications of Isotope Effects in the Determination of Organic Reaction Mechanisms. ADVANCES IN PHYSICAL ORGANIC CHEMISTRY 2012. [DOI: 10.1016/b978-0-12-398484-5.00002-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
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28
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Chan J, Tang A, Bennet AJ. A Stepwise Solvent-Promoted SNi Reaction of α-d-Glucopyranosyl Fluoride: Mechanistic Implications for Retaining Glycosyltransferases. J Am Chem Soc 2011; 134:1212-20. [DOI: 10.1021/ja209339j] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jefferson Chan
- Department
of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC V5A 1S6,
Canada
| | - Ariel Tang
- Department
of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC V5A 1S6,
Canada
| | - Andrew J. Bennet
- Department
of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC V5A 1S6,
Canada
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29
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Pierdominici-Sottile G, Horenstein NA, Roitberg AE. Free energy study of the catalytic mechanism of Trypanosoma cruzi trans-sialidase. From the Michaelis complex to the covalent intermediate. Biochemistry 2011; 50:10150-8. [PMID: 22007596 DOI: 10.1021/bi2009618] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Trypanosoma cruzi trans-sialidase (TcTS) is a crucial enzyme for the infection of Trypanosoma cruzi, the protozoa responsible for Chagas' disease in humans. It catalyzes the transfer of sialic acids from the host's glycoconjugates to the parasite's glycoconjugates. Based on kinetic isotope effect (KIE) studies, a strong nucleophilic participation at the transition state could be determined, and recently, elaborate experiments used 2-deoxy-2,3-difluorosialic acid as substrate and were able to trap a long-lived covalent intermediate (CI) during the catalytic mechanism. In this paper, we compute the KIE and address the entire mechanistic pathway of the CI formation step in TcTS using computational tools. Particularly, the free energy results indicate that in the transition state there is a strong nucleophilic participation of Tyr342, and after this, the system collapsed into a stable CI. We find that there is no carbocation intermediate for this reaction. By means of the energy decomposition method, we identify the residues that have the biggest influence on catalysis. This study facilitates the understanding of the catalytic mechanism of TcTS and can serve as a guide for future inhibitor design studies.
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Affiliation(s)
- Gustavo Pierdominici-Sottile
- Centro de Estudios e Investigaciones, Universidad Nacional de Quilmes, Sáenz Peña 352, B1876BXD Bernal, Argentina
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30
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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: 165] [Impact Index Per Article: 12.7] [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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31
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Lee SS, Hong SY, Errey JC, Izumi A, Davies GJ, Davis BG. Mechanistic evidence for a front-side, SNi-type reaction in a retaining glycosyltransferase. Nat Chem Biol 2011; 7:631-8. [DOI: 10.1038/nchembio.628] [Citation(s) in RCA: 122] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2010] [Accepted: 06/10/2011] [Indexed: 01/14/2023]
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32
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Na Y, Shen H, Byers LD. N-phenylglucosylamine hydrolysis: a mechanistic probe of β-glucosidase. Bioorg Chem 2011; 39:111-3. [PMID: 21435675 DOI: 10.1016/j.bioorg.2011.02.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2010] [Revised: 02/08/2011] [Accepted: 02/21/2011] [Indexed: 11/26/2022]
Abstract
The spontaneous hydrolysis of glycosylamines, where the aglycone is either a primary amine or ammonia, is over a hundred million-times faster than that of O- or S-glycosides. The reason for this (as pointed out by Capon and Connett in 1965) is that, in contrast to the mechanism for O- or S-glycoside hydrolysis, hydrolysis of these N-glycosides (e.g., glc-NHR) involves an endocyclic C-O bond cleavage resulting in formation of an imine (iminium ion) which then reacts with water. Since ring-opening is kinetically favored with glycosylamines, compounds such as phenylglucosylamine can be a useful probes of enzymes that have been suggested to possibly follow this mechanism. With β-glucosidase from sweet almonds, the enzyme is highly efficient in catalyzing the hydrolysis of phenyl glucoside (k(cat)/k(non)∼10(14)) and phenyl thioglucoside (k(cat)/k(non)∼10(10)) while with either the almond or the Aspergillus niger enzyme or with yeast α-glucosidase, there is no detectable catalysis of phenylglucosylamine hydrolysis (k(cat)/k(non)<20). These results are consistent with the generally accepted mechanism involving exocyclic bond cleavage by these enzymes.
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Affiliation(s)
- Ying Na
- Department of Chemistry, Tulane University, New Orleans, LA 70118, USA
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33
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Thibodeaux CJ, Liu HW. Mechanistic studies of 1-aminocyclopropane-1-carboxylate deaminase: characterization of an unusual pyridoxal 5'-phosphate-dependent reaction. Biochemistry 2011; 50:1950-62. [PMID: 21244019 DOI: 10.1021/bi101927s] [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
1-Aminocyclopropane-1-carboxylic acid (ACC) deaminase (ACCD) is a pyridoxal 5'-phosphate (PLP)-dependent enzyme that cleaves the cyclopropane ring of ACC, to give α-ketobutyric acid and ammonia as products. The cleavage of the C(α)-C(β) bond of an amino acid substrate is a rare event in PLP-dependent enzyme catalysis. Potential chemical mechanisms involving nucleophile- or acid-catalyzed cyclopropane ring opening have been proposed for the unusual transformation catalyzed by ACCD, but the actual mode of cyclopropane ring cleavage remains obscure. In this report, we aim to elucidate the mechanistic features of ACCD catalysis by investigating the kinetic properties of ACCD from Pseudomonas sp. ACP and several of its mutant enzymes. Our studies suggest that the pK(a) of the conserved active site residue, Tyr294, is lowered by a hydrogen bonding interaction with a second conserved residue, Tyr268. This allows Tyr294 to deprotonate the incoming amino group of ACC to initiate the aldimine exchange reaction between ACC and the PLP coenzyme and also likely helps to activate Tyr294 for a role as a nucleophile to attack and cleave the cyclopropane ring of the substrate. In addition, solvent kinetic isotope effect (KIE), proton inventory, and (13)C KIE studies of the wild type enzyme suggest that the C(α)-C(β) bond cleavage step in the chemical mechanism is at least partially rate-limiting under k(cat)/K(m) conditions and is likely preceded in the mechanism by a partially rate-limiting step involving the conversion of a stable gem-diamine intermediate into a reactive external aldimine intermediate that is poised for cyclopropane ring cleavage. When viewed within the context of previous mechanistic and structural studies of ACCD enzymes, our studies are most consistent with a mode of cyclopropane ring cleavage involving nucleophilic catalysis by Tyr294.
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Affiliation(s)
- Christopher J Thibodeaux
- Division of Medicinal Chemistry, College of Pharmacy, Department of Chemistry and Biochemistry, and Institute for Cellular and Molecular Biology, University of Texas, Austin, Texas 78712, United States
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34
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A direct NMR method for the measurement of competitive kinetic isotope effects. Nat Chem Biol 2010; 6:405-7. [DOI: 10.1038/nchembio.352] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2009] [Accepted: 02/04/2010] [Indexed: 11/08/2022]
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35
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Golden EB, Byers LD. Methyl glucoside hydrolysis catalyzed by β-glucosidase. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2009; 1794:1643-7. [DOI: 10.1016/j.bbapap.2009.07.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2009] [Revised: 07/17/2009] [Accepted: 07/23/2009] [Indexed: 10/20/2022]
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36
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Botosoa EP, Blumenstein C, MacKenzie DA, Silvestre V, Remaud GS, Kwiecień RA, Robins RJ. Quantitative isotopic 13C nuclear magnetic resonance at natural abundance to probe enzyme reaction mechanisms via site-specific isotope fractionation: The case of the chain-shortening reaction for the bioconversion of ferulic acid to vanillin. Anal Biochem 2009; 393:182-8. [DOI: 10.1016/j.ab.2009.06.031] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2009] [Revised: 05/18/2009] [Accepted: 06/24/2009] [Indexed: 10/20/2022]
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37
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Mauve C, Bleton J, Bathellier C, Lelarge-Trouverie C, Guérard F, Ghashghaie J, Tchapla A, Tcherkez G. Kinetic 12C/13C isotope fractionation by invertase: evidence for a small in vitro isotope effect and comparison of two techniques for the isotopic analysis of carbohydrates. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2009; 23:2499-2506. [PMID: 19603465 DOI: 10.1002/rcm.4068] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
The natural (13)C/(12)C isotope composition (delta(13)C) of plants and organic compounds within plant organs is a powerful tool to understand carbon allocation patterns and the regulation of photosynthetic or respiratory metabolism. However, many enzymatic fractionations are currently unknown, thus impeding our understanding of carbon trafficking pathways within plant cells. One of them is the (12)C/(13)C isotope effect associated with invertases (EC 3.2.1.26) that are cornerstone enzymes for Suc metabolism and translocation in plants. Another conundrum of isotopic plant biology is the need to measure accurately the specific delta(13)C of individual carbohydrates. Here, we examined two complementary methods for measuring the delta(13)C value of sucrose, glucose and fructose, that is, off-line high-performance liquid chromatography (HPLC) purification followed by elemental analysis and isotope ratio mass spectrometry (EA-IRMS) analysis, and gas chromatography-combustion (GC-C)-IRMS. We also used these methods to determine the in vitro (12)C/(13)C isotope effect associated with the yeast invertase. Our results show that, although providing more variable values than HPLC approximately EA-IRMS, and being sensitive to derivatization conditions, the GC-C-IRMS method gives reliable results. When applied to the invertase reaction, both methods indicate that the (12)C/(13)C isotope effect is rather small and it is not affected by the use of heavy water (D(2)O).
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Affiliation(s)
- Caroline Mauve
- Plateforme Métabolisme Métabolome, IFR87 La Plante et son Environnement, Institut de Biotechnologie des Plantes, Université Paris-Sud XI, 91405 Orsay cedex, France
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38
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Computational studies of the role of glycopyranosyl oxacarbenium ions in glycobiology and glycochemistry. Adv Carbohydr Chem Biochem 2009; 62:83-159. [PMID: 19501705 DOI: 10.1016/s0065-2318(09)00004-3] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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39
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Vocadlo DJ, Davies GJ. Mechanistic insights into glycosidase chemistry. Curr Opin Chem Biol 2009; 12:539-55. [PMID: 18558099 DOI: 10.1016/j.cbpa.2008.05.010] [Citation(s) in RCA: 300] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2008] [Accepted: 05/19/2008] [Indexed: 11/16/2022]
Abstract
The enzymatic hydrolysis of the glycosidic bond continues to gain importance, reflecting the critically important roles complex glycans play in health and disease as well as the rekindled interest in enzymatic biomass conversion. Recent advances include the broadening of our understanding of enzyme reaction coordinates, through both computational and structural studies, improved understanding of enzyme inhibition through transition state mimicry and fascinating insights into mechanism yielded by physical organic chemistry approaches.
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Affiliation(s)
- David J Vocadlo
- Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, V5A 1S6, Canada.
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40
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Łysek R, Favre S, Vogel P. Conduramine F-1 epoxides: synthesis and their glycosidase inhibitory activities. Tetrahedron 2007. [DOI: 10.1016/j.tet.2007.03.149] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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41
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Whitfield DM. DFT studies of the ionization of alpha and beta glycopyranosyl donors. Carbohydr Res 2007; 342:1726-40. [PMID: 17555731 DOI: 10.1016/j.carres.2007.05.012] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2007] [Revised: 04/26/2007] [Accepted: 05/06/2007] [Indexed: 11/28/2022]
Abstract
Current attempts at mimicking the transition states (TSs) of glycosyl processing enzymes (GPEs) that proceed through TSs with a high degree of oxacarbenium ion formation suffer from a paucity of data about the conformations of such oxacarbenium ions. Because TSs are maxima, the current models based on minimized structures may need some refinement. As part of studies directed at optimizing chemical glycosylation the ionization of 3,4,6-tri-O-acetyl-alpha/beta-D-glucopyranosyl chlorides and triflates, 2,3,4,6-tetra-O-methyl-alpha/beta-D-glucopyranosyl fluorides, chlorides and triflates, 2,3,4,6-tetra-O-methyl-alpha/beta-D-mannopyranosyl fluorides, 2,3-di-O-methyl 4,6-O-benzylidene alpha/beta-D-mannopyranosyl triflates and 2,3-di-O-methyl 4,6-O-benzylidene alpha/beta-D-glucopyranosyl triflates was studied by a prototypic density functional theory (DFT) procedure. In all cases, the alpha-anomers ionized smoothly to 4H3 half chair conformations or adjacent envelopes. By contrast, all beta-anomers exhibited an abrupt conformational change before ionization was complete. The nature of the conformations sampled depends on both the leaving group and the protecting group. The methods presented can be readily adapted to the study of any GPE or chemical glycosylation and provide a method for initial evaluation of plausible TSs, which in turn can be used in mimetic design.
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Affiliation(s)
- Dennis M Whitfield
- Institute for Biological Sciences, NRC Canada, 100 Sussex Drive, Ottawa, ON, Canada K1A 0R6.
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Tenailleau E, Akoka S. Adiabatic 1H decoupling scheme for very accurate intensity measurements in 13C NMR. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2007; 185:50-8. [PMID: 17142076 DOI: 10.1016/j.jmr.2006.11.007] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2006] [Revised: 11/10/2006] [Accepted: 11/16/2006] [Indexed: 05/12/2023]
Abstract
Adiabatic proton decoupling has been optimized in order to obtain accurate quantitative measurements of intensities on 13C NMR spectra. For each offset, the minimum adiabaticity factor (Km) reached during the pulse was computed. This K(m) profile was used to optimize the peak value and the swept frequency range of the adiabatic pulses. With a cosinus amplitude modulation, offset-independent-adiabaticity, and the M4P5-M4P9-M4P5'-M4P9' phase cycle, an accuracy of 2 per thousand for the 13C NMR measurements was reached. An approach using bi-labeled 13C acetic acid and ethanol at 99% allowed a fine experimental determination of the uniformity of the decoupling profile. The comparison with WALTZ-16 highlights the improvements in the uniformity of the proton decoupling.
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Affiliation(s)
- Eve Tenailleau
- LAIEM-CNRS UMR 6006, Faculté des Sciences et Techniques-Université de NANTES, 2 rue de la Houssinière-BP 92208, 44322 NANTES cedex 3, France
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Abstract
Two isomeric bicyclo[4.1.0]heptane analogues of the glycosidase inhibitor galacto-validamine, (1R*,2S,3S,4S,5S,6S*)-5-amino-1-(hydroxymethyl)bicyclo[4.1.0]heptane-2,3,4-triol, have been synthesized in 13 steps from 2,3,4,6-tetra-O-benzyl-D-galactose. The inhibitory activities of the two conformationally restricted amines, and their corresponding acetamides, were measured against commercial alpha-galactosidase enzymes from coffee bean and E. coli. The activity of the glycosyl hydrolase family GH27 enzyme (coffee bean) was competitively inhibited by the 1R,6S-amine (7), a binding interaction that was characterized by a K(i) value of 0.541 microM. The GH36 E. coli alpha-galactosidase exhibited a much weaker binding interaction with the 1R,6S-amine (IC(50)= 80 microM). The diastereomeric 1S,6R-amine (9) bound weakly to both galactosidases, (coffee bean, IC(50)= 286 microM) and (E. coli, IC(50)= 2.46 mM).
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Affiliation(s)
- Yi Wang
- Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, V5A 1S6, British Columbia, Canada.
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Brecker L, Kögl MF, Tyl CE, Kratzer R, Nidetzky B. NMR study of 13C-kinetic isotope effects at 13C natural abundance to characterize oxidations and an enzyme-catalyzed reduction. Tetrahedron Lett 2006. [DOI: 10.1016/j.tetlet.2006.03.194] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Berti PJ, McCann JAB. Toward a detailed understanding of base excision repair enzymes: transition state and mechanistic analyses of N-glycoside hydrolysis and N-glycoside transfer. Chem Rev 2006; 106:506-55. [PMID: 16464017 DOI: 10.1021/cr040461t] [Citation(s) in RCA: 211] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Paul J Berti
- Department of Chemistry, McMaster University, Hamilton, Ontario, Canada.
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Buser S, Vasella A. Norbornane Mimics of Distortedβ-D-Glucopyranosides – Inhibitors ofβ-D-Glucopyranosidases? Helv Chim Acta 2006. [DOI: 10.1002/hlca.200690064] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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47
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Mechanisms for nucleophilic aliphatic substitution at glycosides. ADVANCES IN PHYSICAL ORGANIC CHEMISTRY 2006. [DOI: 10.1016/s0065-3160(06)41005-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/05/2023]
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van Well R, Ravindranathan Kartha K, Field R. Iodine Promoted Glycosylation with Glycosyl Iodides: α‐Glycoside Synthesis. J Carbohydr Chem 2005. [DOI: 10.1081/car-200067028] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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O'donnell AH, Yao X, Byers LD. Solvent isotope effects on alpha-glucosidase. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2005; 1703:63-7. [PMID: 15588703 DOI: 10.1016/j.bbapap.2004.09.018] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2004] [Revised: 09/15/2004] [Accepted: 09/21/2004] [Indexed: 11/26/2022]
Abstract
The solvent kinetic isotope effects (SKIE) on the yeast alpha-glucosidase-catalyzed hydrolysis of p-nitrophenyl and methyl-d-glucopyranoside were measured at 25 degrees C. With p-nitrophenyl-D-glucopyranoside (pNPG), the dependence of k(cat)/K(m) on pH (pD) revealed an unusually large (for glycohydrolases) solvent isotope effect on the pL-independent second-order rate constant, (DOD)(k(cat)/K(m)), of 1.9 (+/-0.3). The two pK(a)s characterizing the pH profile were increased in D(2)O. The shift in pK(a2) of 0.6 units is typical of acids of comparable acidity (pK(a)=6.5), but the increase in pK(a1) (=5.7) of 0.1 unit in going from H(2)O to D(2)O is unusually small. The initial velocities show substrate inhibition (K(is)/K(m) approximately 200) with a small solvent isotope effect on the inhibition constant [(DOD)K(is)=1.1 (+/-0.2)]. The solvent equilibrium isotope effects on the K(is) for the competitive inhibitors D-glucose and alpha-methyl D-glucoside are somewhat higher [(DOD)K(i)=1.5 (+/-0.1)]. Methyl glucoside is much less reactive than pNPG, with k(cat) 230 times lower and k(cat)/K(m) 5 x 10(4) times lower. The solvent isotope effect on k(cat) for this substrate [=1.11 (+/-0. 02)] is lower than that for pNPG [=1.67 (+/-0.07)], consistent with more extensive proton transfer in the transition state for the deglucosylation step than for the glucosylation step.
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Affiliation(s)
- Anne H O'donnell
- Department of Chemistry, Tulane University, New Orleans, LA 70118, USA
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Vo LK, Singleton DA. Isotope Effects and the Nature of Stereo- and Regioselectivity in Hydroaminations of Vinylarenes Catalyzed by Palladium(II)−Diphosphine Complexes. Org Lett 2004; 6:2469-72. [PMID: 15228306 DOI: 10.1021/ol049137a] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
[reaction: see text] The hydroamination of styrene with aniline catalyzed by phosphine-ligated palladium triflates exhibits a substantial (13)C isotope effect at the benzylic carbon. This supports rate-determining nucleophilic attack of amine on a eta(3)-phenethyl palladium complex. Deuterium exchange observations and predicted isotope effects based on DFT calculations support this mechanism. Selectivity in these reactions is determined by the facility of palladium displacement after reversible hydropalladation of the alkene.
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Affiliation(s)
- Loan K Vo
- Department of Chemistry, Texas A and M University, P.O. Box 30012, College Station, Texas 77842, USA
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