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Svatunek D. Computational Organic Chemistry: The Frontier for Understanding and Designing Bioorthogonal Cycloadditions. Top Curr Chem (Cham) 2024; 382:17. [PMID: 38727989 PMCID: PMC11087259 DOI: 10.1007/s41061-024-00461-0] [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: 11/08/2023] [Accepted: 04/06/2024] [Indexed: 05/13/2024]
Abstract
Computational organic chemistry has become a valuable tool in the field of bioorthogonal chemistry, offering insights and aiding in the progression of this branch of chemistry. In this review, I present an overview of computational work in this field, including an exploration of both the primary computational analysis methods used and their application in the main areas of bioorthogonal chemistry: (3 + 2) and [4 + 2] cycloadditions. In the context of (3 + 2) cycloadditions, detailed studies of electronic effects have informed the evolution of cycloalkyne/1,3-dipole cycloadditions. Through computational techniques, researchers have found ways to adjust the electronic structure via hyperconjugation to enhance reactions without compromising stability. For [4 + 2] cycloadditions, methods such as distortion/interaction analysis and energy decomposition analysis have been beneficial, leading to the development of bioorthogonal reactants with improved reactivity and the creation of orthogonal reaction pairs. To conclude, I touch upon the emerging fields of cheminformatics and machine learning, which promise to play a role in future reaction discovery and optimization.
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Affiliation(s)
- Dennis Svatunek
- Institute of Applied Synthetic Chemistry, Technische Universität Wien (TU Wien), Getreidemarkt 9, 1060, Vienna, Austria.
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Shen YH, Esper AM, Ghiviriga I, Abboud KA, Schanze KS, Ehm C, Veige AS. SPAAC iClick: progress towards a bioorthogonal reaction in-corporating metal ions. Dalton Trans 2021; 50:12681-12691. [PMID: 34545891 DOI: 10.1039/d1dt02626g] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Combining strain-promoted azide-alkyne cycloaddition (SPAAC) and inorganic click (iClick) reactivity provides access to metal 1,2,3-triazolates. Experimental and computational insights demonstrate that iClick reactivity of the tested metal azides (LM-N3, M = Au, W, Re, Ru and Pt) depends on the accessibility of the azide functionality rather than electronic effects imparted by the metal. SPAAC iClick reactivity with cyclooctyne is observed when the azide functionality is sterically unencumbered, e.g. [Au(N3)(PPh3)] (Au-N3), [W(η3-allyl)(N3)(bpy)(CO)2] (W-N3), and [Re(N3)(bpy)(CO)3] [bpy = 2,2'-bipyridine] (Re-N3). Increased steric bulk and/or preequilibria with high activation barriers prevent SPAAC iClick reactivity for the complexes [Ru(N3)(Tp)(PPh3)2] [Tp = tris(pyrazolyl)borate] (Ru-N3), [Pt(N3)(CH3)(PiPr3)2] [iPr = isopropyl] (Pt(II)-N3), and [Pt(N3)(CH3)3]4 ((PtN3)4). Based on these computational insights, the SPAAC iClick reactivity of [Pt(N3)(CH3)3(P(CH3)3)2] (Pt(IV)-N3) was successfully predicted.
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Affiliation(s)
- Yu-Hsuan Shen
- University of Florida, Department of Chemistry, Center for Catalysis, P.O. Box 117200, Gainesville, FL, 32611, USA.
| | - Alec M Esper
- University of Florida, Department of Chemistry, Center for Catalysis, P.O. Box 117200, Gainesville, FL, 32611, USA.
| | - Ion Ghiviriga
- University of Florida, Department of Chemistry, Center for Catalysis, P.O. Box 117200, Gainesville, FL, 32611, USA.
| | - Khalil A Abboud
- University of Florida, Department of Chemistry, Center for Catalysis, P.O. Box 117200, Gainesville, FL, 32611, USA.
| | - Kirk S Schanze
- University of Texas at San Antonio, Department of Chemistry, One UTSA Circle, San Antonio, TX 78249, USA
| | - Christian Ehm
- Dipartimento di Scienze Chimiche, Università di Napoli Federico II, Via Cintia, 80126 Napoli, Italy.
| | - Adam S Veige
- University of Florida, Department of Chemistry, Center for Catalysis, P.O. Box 117200, Gainesville, FL, 32611, USA.
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Hamzehloueian M, Hosseinzadeh R, Ghandiyar S. A theoretical study on the metal-free triazole formation through tandem [3+2] cycloaddition/retro-Diels-Alder reaction of benzyl azide and oxanorbornadienedicarboxylate. J Mol Graph Model 2020; 97:107552. [DOI: 10.1016/j.jmgm.2020.107552] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 01/23/2020] [Accepted: 01/27/2020] [Indexed: 10/25/2022]
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Interplay of thermochemistry and Structural Chemistry, the journal (volume 28, 2017, issues 5–6), and the discipline. Struct Chem 2018. [DOI: 10.1007/s11224-018-1217-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Hamzehloueian M, Davari Z. Mechanism and origins of the regioselectivity in the [3+2] cycloaddition reaction of an azomethine ylide with benzoimidazole-2-yl-3-phenylacrilonitrile: A DFT approach. J Mol Graph Model 2018; 80:32-37. [DOI: 10.1016/j.jmgm.2017.12.019] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Revised: 12/26/2017] [Accepted: 12/28/2017] [Indexed: 10/18/2022]
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