1
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Das E, Feliciano MAM, Yamanushkin P, Lin X, Gold B. Oxa-azabenzobenzocyclooctynes (O-ABCs): heterobiarylcyclooctynes bearing an endocyclic heteroatom. Org Biomol Chem 2023; 21:8857-8862. [PMID: 37881858 DOI: 10.1039/d3ob01559a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2023]
Abstract
We report the synthesis of heterobiarylcyclooctynes bearing an endocyclic heteroatom, oxa-azabenzobenzocyclooctynes (O-ABCs). The integration of design strategies for accelerating strain-promoted azide-alkyne cycloadditions results in reactivity with organic azides that surpasses all cyclooctyne reagents reported to date. O-ABCs and related compounds provide insights into the effects of structural modifications on reactivity that can aid in the design of new reagents for click and bioorthogonal chemistry.
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Affiliation(s)
- Eshani Das
- Department of Chemistry and Chemical Biology, University of New Mexico, New Mexico, 87131, USA
| | - Mark Aldren M Feliciano
- Department of Chemistry and Biochemistry, New Mexico State University, Las Cruces, New Mexico, 88003, USA.
- Department of Chemistry and Chemical Biology, University of New Mexico, New Mexico, 87131, USA
| | - Pavel Yamanushkin
- Department of Chemistry and Chemical Biology, University of New Mexico, New Mexico, 87131, USA
| | - Xinsong Lin
- Department of Chemistry and Biochemistry Florida State University, Tallahassee, FL, 32306, USA
| | - Brian Gold
- Department of Chemistry and Biochemistry, New Mexico State University, Las Cruces, New Mexico, 88003, USA.
- Department of Chemistry and Chemical Biology, University of New Mexico, New Mexico, 87131, USA
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2
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Holzmann MJ, Khanal N, Yamanushkin P, Gold B. Remote Strain Activation in a Sulfate-Linked Dibenzocycloalkyne. Org Lett 2023; 25:309-313. [PMID: 36455206 DOI: 10.1021/acs.orglett.2c03397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Cycloalkynes and their utilization in cycloaddition reactions enable modular strategies spanning the molecular sciences. Strain─imparted by deviation from linearity─enables sufficient alkyne reactivity without the need for a catalyst (e.g., copper); however, the design and synthesis of stable reagents with suitable reactivity remains an ongoing challenge. We report the incorporation of an endocyclic sulfate within a dibenzocyclononyne scaffold to generate a cyclononyne displaying remarkable reactivity and stability. Through computational analyses, we revealed that the endocyclic sulfate group shares nearly half the total strain energy, providing an activation strategy that reduces alkyne bending. Rehybridization of alkyne carbons in the formation of the heterocyclic product relieves strain both at the reactive site and in the transannular sulfate group. This mode of remote activation enables rapid reactivity while minimizing distortion─and strain─at the reactive site (the alkyne). The result: a design strategy for a new class of cycloalkynes with increased stability and reactivity.
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Affiliation(s)
- Michael J Holzmann
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131, United States
| | - Namrata Khanal
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131, United States
| | - Pavel Yamanushkin
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131, United States
| | - Brian Gold
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131, United States
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3
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Escorihuela J. A Density Functional Theory Study on the Cobalt-Mediated Intramolecular Pauson–Khand Reaction of Enynes Containing a Vinyl Fluoride Moiety. SYNTHESIS-STUTTGART 2022. [DOI: 10.1055/s-0042-1751392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
AbstractThe Co2(CO)8-mediated intramolecular Pauson–Khand reaction (PKR) is an effective method for constructing polycyclic structures. Recently, our group reported a series of this type of reaction involving fluorinated enynes that proceed with reasonable reaction rates and yields. However, mechanistic studies involving these fluorinated derivatives in intramolecular PKR are scarce. In this study, density functional theory calculations are used to clarify the mechanism and reactivity of enynes containing a vinyl fluoride moiety for this reaction. In agreement with previous studies, alkene insertion is considered to be the rate-determining step for the overall Pauson–Khand reaction of enynes containing a vinyl fluoride moiety. The effect of the substituent on the Co2(CO)8-mediated intramolecular Pauson–Khand reaction has also been investigated. When introducing heteroatoms as tethering units, the fluorinated enynes exhibited lower reactivity than the malonate homologues, whereas the use of a sulfur-based tether was unsuccessful. This computational study provides detailed information about the PKR mechanism and transition-state structures, and the results are validated with previous experimental results.
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4
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Dones JM, Abularrage NS, Khanal N, Gold B, Raines RT. Acceleration of 1,3-Dipolar Cycloadditions by Integration of Strain and Electronic Tuning. J Am Chem Soc 2021; 143:9489-9497. [PMID: 34151576 DOI: 10.1021/jacs.1c03133] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
The 1,3-dipolar cycloaddition between azides and alkynes provides new means to probe and control biological processes. A major challenge is to achieve high reaction rates with stable reagents. The optimization of alkynyl reagents has relied on two strategies: increasing strain and tuning electronics. We report on the integration of these strategies. A computational analysis suggested that a CH → N aryl substitution in dibenzocyclooctyne (DIBO) could be beneficial. In transition states, the nitrogen of 2-azabenzo-benzocyclooctyne (ABC) engages in an n→π* interaction with the C=O of α-azidoacetamides and forms a hydrogen bond with the N-H of α-diazoacetamides. These dipole-specific interactions act cooperatively with electronic activation of the strained π-bond to increase reactivity. We found that ABC does indeed react more quickly with α-azidoacetamides and α-diazoacetamides than its constitutional isomer, dibenzoazacyclooctyne (DIBAC). ABC and DIBAC have comparable chemical stability in a biomimetic solution. Both ABC and DIBO are accessible in three steps by the alkylidene carbene-mediated ring expansion of commercial cycloheptanones. Our findings enhance the accessibility and utility of 1,3-dipolar cycloadditions and encourage further innovation.
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Affiliation(s)
- Jesús M Dones
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Nile S Abularrage
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Namrata Khanal
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131, United States
| | - Brian Gold
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States.,Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131, United States
| | - Ronald T Raines
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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5
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Hu Y, Roberts JM, Kilgore HR, Lani ASM, Raines RT, Schomaker JM. Triple, Mutually Orthogonal Bioorthogonal Pairs through the Design of Electronically Activated Sulfamate-Containing Cycloalkynes. J Am Chem Soc 2020; 142:18826-18835. [PMID: 33085477 PMCID: PMC7891878 DOI: 10.1021/jacs.0c06725] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Interest in mutually exclusive pairs of bioorthogonal labeling reagents continues to drive the design of new compounds that are capable of fast and predictable reactions. The ability to easily modify S-, N-, and O-containing cyclooctynes (SNO-OCTs) enables electronic tuning of various SNO-OCTs to influence their cycloaddition rates with Type I-III dipoles. As opposed to optimizations based on just one specific dipole class, the electrophilicity of the alkynes in SNO-OCTs can be manipulated to achieve divergent reactivities and furnish mutually orthogonal dual ligation systems. Significant reaction rate enhancements of a difluorinated SNO-OCT derivative, as compared to the parent scaffold, were noted, with the second-order rate constant in cycloadditions with diazoacetamides exceeding 5.13 M-1 s-1. Computational and experimental studies were employed to inform the design of triple ligation systems that encompass three orthogonal reactivities. Finally, polar SNO-OCTs are rapidly internalized by mammalian cells and remain functional in the cytosol for live-cell labeling, highlighting their potential for diverse in vitro and in vivo applications.
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Affiliation(s)
- Yun Hu
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, United States
| | - Jessica M. Roberts
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, United States
| | - Henry R. Kilgore
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Amirah S. Mat Lani
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, United States
| | - Ronald T. Raines
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Jennifer M. Schomaker
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, United States
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6
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Bettens T, Alonso M, Geerlings P, De Proft F. The hunt for reactive alkynes in bio-orthogonal click reactions: insights from mechanochemical and conceptual DFT calculations. Chem Sci 2019; 11:1431-1439. [PMID: 34123268 PMCID: PMC8148320 DOI: 10.1039/c9sc04507d] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
In our effort to implement the mechanical force used to activate single molecules in mechanochemistry in the context of conceptual density functional theory, we present a theoretical investigation of strained alkynes for rationalizing structural trends as well as the reactivity of cyclic alkynes that are of great importance in in vivo click reactions. The strain on the triple bond in cyclic alkynes is modeled by angular constraints in a 2-butyne fragment and the corresponding bending force is calculated by means of an extended COGEF (constrained geometries simulate external forces) model. In general, the force required to bend the triple bond is smaller with electron-withdrawing groups on the propargylic C-atom, which elegantly results in smaller angles around the triple bond in cyclic alkynes with such substitution pattern. By means of conceptual DFT descriptors, the electrophilic and nucleophilic character of bent triple bonds was investigated revealing moderate activation for small distortions from the linear geometry (0° to 15°) and a drastically more reactive π-space if the triple bond is bent further. This analysis of the intrinsic reactivity of the triple bond is in line with experimental observations, explaining the reactive nature of cyclooctynes and cycloheptynes, whereas larger cyclic systems do not drastically activate the triple bond.
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Affiliation(s)
- Tom Bettens
- Eenheid Algemene Chemie (ALGC), Vrije Universiteit Brussel (VUB) Pleinlaan 2 1050 Brussels Belgium
| | - Mercedes Alonso
- Eenheid Algemene Chemie (ALGC), Vrije Universiteit Brussel (VUB) Pleinlaan 2 1050 Brussels Belgium
| | - Paul Geerlings
- Eenheid Algemene Chemie (ALGC), Vrije Universiteit Brussel (VUB) Pleinlaan 2 1050 Brussels Belgium
| | - Frank De Proft
- Eenheid Algemene Chemie (ALGC), Vrije Universiteit Brussel (VUB) Pleinlaan 2 1050 Brussels Belgium
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7
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Zhao J, Li H, Li P, Wang L. Annulation of Benzamides with Arynes Using Palladium with Photoredox Dual Catalysis. J Org Chem 2019; 84:9007-9016. [DOI: 10.1021/acs.joc.9b00893] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Jie Zhao
- Department of Chemistry, Huaibei Normal University, Huaibei, Anhui 235000, P. R. China
| | - Hongji Li
- Department of Chemistry, Huaibei Normal University, Huaibei, Anhui 235000, P. R. China
| | - Pinhua Li
- Department of Chemistry, Huaibei Normal University, Huaibei, Anhui 235000, P. R. China
| | - Lei Wang
- Department of Chemistry, Huaibei Normal University, Huaibei, Anhui 235000, P. R. China
- State Key Laboratory of Organometallic Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, P. R. China
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8
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Harris T, Alabugin IV. Strain and stereoelectronics in cycloalkyne click chemistry. MENDELEEV COMMUNICATIONS 2019. [DOI: 10.1016/j.mencom.2019.05.001] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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9
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Hamlin TA, Svatunek D, Yu S, Ridder L, Infante I, Visscher L, Bickelhaupt FM. Elucidating the Trends in Reactivity of Aza-1,3-Dipolar Cycloadditions. European J Org Chem 2018. [DOI: 10.1002/ejoc.201800572] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Trevor A. Hamlin
- Department of Theoretical Chemistry and Amsterdam Center for Multiscale Modeling (ACMM); Vrije Universiteit Amsterdam; De Boelelaan 1083 1081 HV Amsterdam The Netherlands
| | - Dennis Svatunek
- Department of Theoretical Chemistry and Amsterdam Center for Multiscale Modeling (ACMM); Vrije Universiteit Amsterdam; De Boelelaan 1083 1081 HV Amsterdam The Netherlands
- Institute of Applied Synthetic Chemistry; Technische Universität Wien (TU Wien); Getreidemarkt 9 1060 Vienna Austria
| | - Song Yu
- Department of Theoretical Chemistry and Amsterdam Center for Multiscale Modeling (ACMM); Vrije Universiteit Amsterdam; De Boelelaan 1083 1081 HV Amsterdam The Netherlands
| | - Lars Ridder
- Netherlands eScience Center; Science Park 140 1098 XG Amsterdam The Netherlands
| | - Ivan Infante
- Institute for Molecules and Materials (IMM); Radboud University; Heyendaalseweg 135 6525 AJ Nijmegen The Netherlands
| | - Lucas Visscher
- Department of Theoretical Chemistry and Amsterdam Center for Multiscale Modeling (ACMM); Vrije Universiteit Amsterdam; De Boelelaan 1083 1081 HV Amsterdam The Netherlands
| | - F. Matthias Bickelhaupt
- Department of Theoretical Chemistry and Amsterdam Center for Multiscale Modeling (ACMM); Vrije Universiteit Amsterdam; De Boelelaan 1083 1081 HV Amsterdam The Netherlands
- Institute for Molecules and Materials (IMM); Radboud University; Heyendaalseweg 135 6525 AJ Nijmegen The Netherlands
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10
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Yoshida S. Controlled Reactive Intermediates Enabling Facile Molecular Conjugation. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2018. [DOI: 10.1246/bcsj.20180104] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Suguru Yoshida
- Laboratory of Chemical Bioscience, Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU), 2-3-10 Kanda-Surugadai, Chiyoda-ku, Tokyo 101-0062, Japan
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11
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Escorihuela J, Das A, Looijen WJE, van Delft FL, Aquino AJA, Lischka H, Zuilhof H. Kinetics of the Strain-Promoted Oxidation-Controlled Cycloalkyne-1,2-quinone Cycloaddition: Experimental and Theoretical Studies. J Org Chem 2018; 83:244-252. [PMID: 29260879 PMCID: PMC5759032 DOI: 10.1021/acs.joc.7b02614] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2017] [Indexed: 11/29/2022]
Abstract
Stimulated by its success in both bioconjugation and surface modification, we studied the strain-promoted oxidation-controlled cycloalkyne-1,2-quinone cycloaddition (SPOCQ) in three ways. First, the second-order rate constants and activation parameters (ΔH⧧) were determined of various cyclooctynes reacting with 4-tert-butyl-1,2-quinone in a SPOCQ reaction, yielding values for ΔH⧧ of 4.5, 7.3, and 12.1 kcal/mol, for bicyclo[6.1.0]non-4-yne (BCN), cyclooctyne (OCT), and dibenzoazacyclooctyne (DIBAC), respectively. Second, their reaction paths were investigated in detail by a range of quantum mechanical calculations. Single-configuration theoretical methods, like various DFT and a range of MP2-based methods, typically overestimate this barrier by 3-8 kcal/mol (after inclusion of zero-point energy, thermal, and solvation corrections), whereas MP2 itself underestimates the barrier significantly. Only dispersion-corrected DFT methods like B97D (yielding 4.9, 6.4, and 12.1 kcal/mol for these three reactions) and high-level CCSD(T) and multireference multiconfiguration AQCC ab initio approaches (both yielding 8.2 kcal/mol for BCN) give good approximations of experimental data. Finally, the multireference methods show that the radical character in the TS is rather small, thus rationalizing the use of single-reference methods like B97D and SCS-MP2 as intrinsically valid approaches.
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Affiliation(s)
- Jorge Escorihuela
- Laboratory
of Organic Chemistry, Wageningen University, Stippeneng 4, 6708 WE Wageningen, The Netherlands
- Escuela
Técnica Superior de Ingenieros Industriales − Departamento
de Termodinámica Aplicada, Universitat
Politècnica de València, Camino de Vera s/n, 46020 Valencia, Spain
| | - Anita Das
- School
of Pharmaceutical Sciences and Technology, Tianjin University, Tianjin 300072, China
| | - Wilhelmus J. E. Looijen
- Laboratory
of Organic Chemistry, Wageningen University, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Floris L. van Delft
- Laboratory
of Organic Chemistry, Wageningen University, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Adelia J. A. Aquino
- School
of Pharmaceutical Sciences and Technology, Tianjin University, Tianjin 300072, China
- Institute
for Soil Research, University of Natural Resources and Life Sciences
Vienna, Peter-Jordan-Strasse
82, A-1190 Vienna, Austria
| | - Hans Lischka
- School
of Pharmaceutical Sciences and Technology, Tianjin University, Tianjin 300072, China
- Institute
for Theoretical Chemistry, University of Vienna, Waehringerstrasse 17, A-1090 Vienna, Austria
| | - Han Zuilhof
- Laboratory
of Organic Chemistry, Wageningen University, Stippeneng 4, 6708 WE Wageningen, The Netherlands
- School
of Pharmaceutical Sciences and Technology, Tianjin University, Tianjin 300072, China
- Department
of Chemical and Materials Engineering, King
Abdulaziz University, Jeddah, Saudi Arabia
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12
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Burke EG, Gold B, Hoang TT, Raines RT, Schomaker JM. Fine-Tuning Strain and Electronic Activation of Strain-Promoted 1,3-Dipolar Cycloadditions with Endocyclic Sulfamates in SNO-OCTs. J Am Chem Soc 2017; 139:8029-8037. [PMID: 28505435 DOI: 10.1021/jacs.7b03943] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The ability to achieve predictable control over the polarization of strained cycloalkynes can influence their behavior in subsequent reactions, providing opportunities to increase both rate and chemoselectivity. A series of new heterocyclic strained cyclooctynes containing a sulfamate backbone (SNO-OCTs) were prepared under mild conditions by employing ring expansions of silylated methyleneaziridines. SNO-OCT derivative 8 outpaced even a difluorinated cyclooctyne in a 1,3-dipolar cycloaddition with benzylazide. The various orbital interactions of the propargylic and homopropargylic heteroatoms in SNO-OCT were explored both experimentally and computationally. The inclusion of these heteroatoms had a positive impact on stability and reactivity, where electronic effects could be utilized to relieve ring strain. The choice of the heteroatom combinations in various SNO-OCTs significantly affected the alkyne geometries, thus illustrating a new strategy for modulating strain via remote substituents. Additionally, this unique heteroatom activation was capable of accelerating the rate of reaction of SNO-OCT with diazoacetamide over azidoacetamide, opening the possibility of further method development in the context of chemoselective, bioorthogonal labeling.
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Affiliation(s)
- Eileen G Burke
- Department of Chemistry and ‡Department of Biochemistry, University of Wisconsin , Madison, Wisconsin 53706, United States
| | - Brian Gold
- Department of Chemistry and ‡Department of Biochemistry, University of Wisconsin , Madison, Wisconsin 53706, United States
| | - Trish T Hoang
- Department of Chemistry and ‡Department of Biochemistry, University of Wisconsin , Madison, Wisconsin 53706, United States
| | - Ronald T Raines
- Department of Chemistry and ‡Department of Biochemistry, University of Wisconsin , Madison, Wisconsin 53706, United States
| | - Jennifer M Schomaker
- Department of Chemistry and ‡Department of Biochemistry, University of Wisconsin , Madison, Wisconsin 53706, United States
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13
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Lauko J, Kouwer PHJ, Rowan AE. 1
H
‐1,2,3‐Triazole: From Structure to Function and Catalysis. J Heterocycl Chem 2016. [DOI: 10.1002/jhet.2770] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Ján Lauko
- Institute for Molecules and MaterialsRadboud University Nijmegen Heyendaalseweg 135 6525 AJ Nijmegen The Netherlands
| | - Paul H. J. Kouwer
- Institute for Molecules and MaterialsRadboud University Nijmegen Heyendaalseweg 135 6525 AJ Nijmegen The Netherlands
| | - Alan E. Rowan
- Institute for Molecules and MaterialsRadboud University Nijmegen Heyendaalseweg 135 6525 AJ Nijmegen The Netherlands
- Australian Institute for Bioengineering and Nanotechnology (AIBN)The University of Queensland Brisbane QLD 4072 Australia
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14
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Gold B, Aronoff MR, Raines RT. Decreasing Distortion Energies without Strain: Diazo-Selective 1,3-Dipolar Cycloadditions. J Org Chem 2016; 81:5998-6006. [PMID: 27332711 PMCID: PMC5141247 DOI: 10.1021/acs.joc.6b00948] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The diazo group has attributes that complement those of the azido group for applications in chemical biology. Here, we use computational analyses to provide insights into the chemoselectivity of the diazo group in 1,3-dipolar cycloadditions. Dipole distortion energies are responsible for ∼80% of the overall energetic barrier for these reactions. Here, we show that diazo compounds, unlike azides, provide an opportunity to decrease that barrier substantially without introducing strain into the dipolarophile. The ensuing rate enhancement is due to the greater nucleophilic character of a diazo group compared to that of an azido group, which can accommodate decreased distortion energies without predistortion. The tuning of distortion energies with substituents in a diazo compound or dipolarophile can enhance reactivity and selectivity in a predictable manner. Notably, these advantages of diazo groups are amplified in water. Our findings provide a theoretical framework that can guide the design and application of both diazo compounds and azides in "orthogonal" contexts, especially for biological investigations.
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Affiliation(s)
- Brian Gold
- Department of Chemistry, University of Wisconsin–Madison, Madison, Wisconsin 53706, United States
| | - Matthew R. Aronoff
- Department of Chemistry, University of Wisconsin–Madison, Madison, Wisconsin 53706, United States
| | - Ronald T. Raines
- Department of Chemistry, University of Wisconsin–Madison, Madison, Wisconsin 53706, United States
- Department of Biochemistry, University of Wisconsin–Madison, Madison, Wisconsin 53706, United States
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15
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Aronoff MR, Gold B, Raines RT. Rapid cycloaddition of a diazo group with an unstrained dipolarophile. Tetrahedron Lett 2016; 57:2347-2350. [PMID: 27909348 PMCID: PMC5125787 DOI: 10.1016/j.tetlet.2016.04.020] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The cycloaddition of a diazoacetamide with ethyl 4,4,4-trifluorocrotonate proceeds with k = 0.1 M-1s-1. This second-order rate constant rivals those of optimized strain-promoted azide- alkyne cycloadditions, even though the reaction does not release strain. The regioselectivity and a computational distortion/interaction analysis of the reaction energetics are consistent with the formation of an N-H…F-C hydrogen bond in the transition state and the electronic character of the trifluorocrotonate. Analogous reactions with an azidoacetamide dipole or with an acrylate or crotonate dipolarophile were much slower. These findings suggest a new strategy for the design of diazo-selective reagents for chemical biology.
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Affiliation(s)
- Matthew R. Aronoff
- Department of Chemistry, University of Wisconsin–Madison, Madison, WI 53706, USA
| | - Brian Gold
- Department of Chemistry, University of Wisconsin–Madison, Madison, WI 53706, USA
| | - Ronald T. Raines
- Department of Chemistry, University of Wisconsin–Madison, Madison, WI 53706, USA
- Department of Biochemistry, University of Wisconsin–Madison, Madison, WI 53706, USA
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16
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Sen R, Escorihuela J, Smulders MMJ, Zuilhof H. Use of Ambient Ionization High-Resolution Mass Spectrometry for the Kinetic Analysis of Organic Surface Reactions. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2016; 32:3412-9. [PMID: 27028705 DOI: 10.1021/acs.langmuir.6b00427] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
In contrast to homogeneous systems, studying the kinetics of organic reactions on solid surfaces remains a difficult task due to the limited availability of appropriate analysis techniques that are general, high-throughput, and capable of offering quantitative, structural surface information. Here, we demonstrate how direct analysis in real time mass spectrometry (DART-MS) complies with above considerations and can be used for determining interfacial kinetic parameters. The presented approach is based on the use of a MS tag that--in principle--allows application to other reactions. To show the potential of DART-MS, we selected the widely applied strain-promoted alkyne-azide cycloaddition (SPAAC) as a model reaction to elucidate the effects of the nanoenvironment on the interfacial reaction rate.
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Affiliation(s)
- Rickdeb Sen
- Laboratory of Organic Chemistry, Wageningen University , Dreijenplein 8, 6703 HB Wageningen, The Netherlands
| | - Jorge Escorihuela
- Laboratory of Organic Chemistry, Wageningen University , Dreijenplein 8, 6703 HB Wageningen, The Netherlands
| | - Maarten M J Smulders
- Laboratory of Organic Chemistry, Wageningen University , Dreijenplein 8, 6703 HB Wageningen, The Netherlands
| | - Han Zuilhof
- Laboratory of Organic Chemistry, Wageningen University , Dreijenplein 8, 6703 HB Wageningen, The Netherlands
- Department of Chemical and Materials Engineering, King Abdulaziz University , Jeddah, Saudi Arabia
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17
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Alabugin IV, Bresch S, dos Passos Gomes G. Orbital hybridization: a key electronic factor in control of structure and reactivity. J PHYS ORG CHEM 2014. [DOI: 10.1002/poc.3382] [Citation(s) in RCA: 92] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Igor V. Alabugin
- Department of Chemistry and Biochemistry; Florida State University; Tallahassee FL 32306-4390 USA
| | - Stefan Bresch
- Department of Chemistry and Biochemistry; Florida State University; Tallahassee FL 32306-4390 USA
| | - Gabriel dos Passos Gomes
- Department of Chemistry and Biochemistry; Florida State University; Tallahassee FL 32306-4390 USA
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MacKenzie DA, Sherratt AR, Chigrinova M, Cheung LLW, Pezacki JP. Strain-promoted cycloadditions involving nitrones and alkynes—rapid tunable reactions for bioorthogonal labeling. Curr Opin Chem Biol 2014; 21:81-8. [DOI: 10.1016/j.cbpa.2014.05.023] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2014] [Revised: 05/17/2014] [Accepted: 05/28/2014] [Indexed: 11/24/2022]
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Gold B, Batsomboon P, Dudley GB, Alabugin IV. Alkynyl Crown Ethers as a Scaffold for Hyperconjugative Assistance in Noncatalyzed Azide–Alkyne Click Reactions: Ion Sensing through Enhanced Transition-State Stabilization. J Org Chem 2014; 79:6221-32. [DOI: 10.1021/jo500958n] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Brian Gold
- Department of Chemistry and
Biochemistry, Florida State University, Tallahassee, Florida 32306-4390, United States
| | - Paratchata Batsomboon
- Department of Chemistry and
Biochemistry, Florida State University, Tallahassee, Florida 32306-4390, United States
| | - Gregory B. Dudley
- Department of Chemistry and
Biochemistry, Florida State University, Tallahassee, Florida 32306-4390, United States
| | - Igor V. Alabugin
- Department of Chemistry and
Biochemistry, Florida State University, Tallahassee, Florida 32306-4390, United States
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20
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MacKenzie DA, Pezacki JP. Kinetics studies of rapid strain-promoted [3+2] cycloadditions of nitrones with bicyclo[6.1.0]nonyne. CAN J CHEM 2014. [DOI: 10.1139/cjc-2013-0577] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Strain-promoted alkyne−nitrone cycloaddition (SPANC) reactions represent a bioorthogonal labeling strategy that is both very rapid and at the same time efficient and selective. Nitrones provide increased reaction rates as well as greater susceptibility toward stereoelectronic modification when compared with organic azides. We find that strain-promoted cycloadditions of cyclic nitrones with bicyclo[6.1.0]nonyne react with second-order rate constants as large as 1.49 L mol−1 s−1 at 25 °C. These reactions display rate constants that are up to 37-fold greater than those of the analogous reactions of benzyl azide with bicyclo[6.1.0]nonyne. We observed that reactions of nitrones with bicyclo[6.1.0]nonyne showed a stronger dependence on substituent effect for the reaction, as evidenced by a larger Hammett ρ value, than that for biaryl-aza-cyclooctanone. We demonstrate the ability to stereoelectronically tune the reactivity of nitrones towards different cyclooctynes in SPANC reactions. This ability to introduce selectivity into different SPANC reactions through substituent provides the opportunity to perform multiple SPANC reactions in one reaction vessel and opens up potential applications in multiplex labeling.
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Affiliation(s)
- Douglas A. MacKenzie
- Life Sciences Division, National Research Council of Canada, 100 Sussex Drive, Ottawa, ON K1A 0R6, Canada; Department of Chemistry, University of Ottawa, 10 Marie-Curie, Ottawa, ON K1N 6N5, Canada
| | - John Paul Pezacki
- Life Sciences Division, National Research Council of Canada, 100 Sussex Drive, Ottawa, ON K1A 0R6, Canada; Department of Chemistry, University of Ottawa, 10 Marie-Curie, Ottawa, ON K1N 6N5, Canada
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21
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Tseng MC, Chu YH. Reaction-Based Azide Gas Sensing with Tailored Ionic Liquids Measured by Quartz Crystal Microbalance. Anal Chem 2014; 86:1949-52. [DOI: 10.1021/ac404011z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Ming-Chung Tseng
- Department of Chemistry and
Biochemistry, National Chung Cheng University 168 University Road, Chiayi 62102, Taiwan, ROC
| | - Yen-Ho Chu
- Department of Chemistry and
Biochemistry, National Chung Cheng University 168 University Road, Chiayi 62102, Taiwan, ROC
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