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Dunning SG, Tang WS, Chen B, Zhu L, Cody GD, Chariton S, Prakapenka VB, Strobel TA. Pressure-Induced Amidine Formation via Side-Chain Polymerization in a Charge-Transfer Cocrystal. J Phys Chem Lett 2024; 15:2344-2351. [PMID: 38387075 DOI: 10.1021/acs.jpclett.3c02582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2024]
Abstract
Compression of small molecules can induce solid-state reactions that are difficult or impossible under conventional, solution-phase conditions. Of particular interest is the topochemical-like reaction of arenes to produce polymeric nanomaterials. However, high reaction onset pressures and poor selectivity remain significant challenges. Herein, the incorporation of electron-withdrawing and -donating groups into π-stacked arenes is proposed as a strategy to reduce reaction barriers to cycloaddition and onset pressures. Nevertheless, competing side-chain reactions between functional groups represent alternative viable pathways. For the case of a diaminobenzene:tetracyanobenzene cocrystal, amidine formation between amine and cyano groups occurs prior to cycloaddition with an onset pressure near 9 GPa, as determined using vibrational spectroscopy, X-ray diffraction, and first-principles calculations. This work demonstrates that reduced-barrier cycloaddition reactions are theoretically possible via strategic functionalization; however, the incorporation of pendant groups may enable alternative reaction pathways. Controlled reactions between pendant groups represent an additional strategy for producing unique polymeric nanomaterials.
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Affiliation(s)
- Samuel G Dunning
- Earth and Planets Laboratory, Carnegie Institution for Science, Washington, D.C. 20015, United States
| | - Wan Si Tang
- Earth and Planets Laboratory, Carnegie Institution for Science, Washington, D.C. 20015, United States
| | - Bo Chen
- Donostia International Physics Center, Paseo Manuel de Lardizabal, 4, 20018 Donostia-San Sebastian, Spain
- IKERBASQUE, Basque Foundation for Science, Plaza Euskadi 5, 48009 Bilbao, Spain
| | - Li Zhu
- Physics Department, Rutgers University-Newark, 101 Warren Street, Newark, New Jersey 07102, United States
| | - George D Cody
- Earth and Planets Laboratory, Carnegie Institution for Science, Washington, D.C. 20015, United States
| | - Stella Chariton
- Center for Advanced Radiation Sources, The University of Chicago, Chicago, Illinois 60637, United States
| | - Vitali B Prakapenka
- Center for Advanced Radiation Sources, The University of Chicago, Chicago, Illinois 60637, United States
| | - Timothy A Strobel
- Earth and Planets Laboratory, Carnegie Institution for Science, Washington, D.C. 20015, United States
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2
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Ayarde-Henríquez L, Guerra C, Duque-Noreña M, Chamorro E. A simple topology-based model for predicting the activation barriers of reactive processes at 0 K. Phys Chem Chem Phys 2023; 25:14274-14284. [PMID: 37183509 DOI: 10.1039/d3cp01008b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
This work reveals an underlying correlation between the topology and energetic features of matter configurations/rearrangements by exploiting two topological concepts, namely, structural stability and persistency, leading thus to a model capable of predicting activation energies at 0 K. This finding provides some answers to the difficulties of applying Thom's functions for extracting energetic information of rate processes, which has been a limitation for exact, biological, and technological sciences. A linear relationship between the experimental barriers of 17 chemical reactions and both concepts was found by studying these systems' topography along the intrinsic reaction coordinate. Such a procedure led to the model , which accurately predicts the activation energy in reacting systems involving organic and organometallic compounds under different conditions, e.g., the gas-phase, solvent media, and temperature. This function was further recalibrated to enhance its predicting capabilities, generating the equation for this procedure, characterized by a squared Pearson correlation coefficient (r2 = 0.9774) 1.1 times higher. Surprisingly, no improvement was observed.
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Affiliation(s)
- Leandro Ayarde-Henríquez
- School of Physics, Trinity College Dublin, College Green Dublin 2, Ireland.
- Centro de Química Teórica & Computacional (CQT&C), Departamento de Ciencias Químicas, Avenida República 275, 8370146, Santiago de Chile, Chile
| | - Cristian Guerra
- Facultad de Ciencias Exactas, Centro de Química Teórica & Computacional (CQT&C), Departamento de Ciencias Químicas, Universidad Andrés Bello, Avenida República 275, 8370146, Santiago de Chile, Chile.
- Facultad de Ciencias Básicas, Grupo de Química Computacional, Universidad de Córdoba, Carrera 6 No. 77-305, Montería, Córdoba, Colombia
| | - Mario Duque-Noreña
- Facultad de Ciencias Exactas, Centro de Química Teórica & Computacional (CQT&C), Departamento de Ciencias Químicas, Universidad Andrés Bello, Avenida República 275, 8370146, Santiago de Chile, Chile.
| | - Eduardo Chamorro
- Facultad de Ciencias Exactas, Centro de Química Teórica & Computacional (CQT&C), Departamento de Ciencias Químicas, Universidad Andrés Bello, Avenida República 275, 8370146, Santiago de Chile, Chile.
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Kinani AABY, Abdulkareem Mahmood E, Shoaei SM, Heravi MRP, Habibzadeh S, Ebadi AG, Amini I, Vessally E. The chemical reaction of thioindole and [20] fullerene and the use of DFT to estimate some quantum chemical descriptors. J Sulphur Chem 2022. [DOI: 10.1080/17415993.2022.2139146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Ahmad AB Yosef Kinani
- Department of pharmaceutics College of pharmacy, Al Farahidi University, Baghdad, Iraq
| | - Evan Abdulkareem Mahmood
- Medical Laboratory Sciences Department, College of Health Sciences, University of Human Development, Sulaymaniyah, Iraq
| | | | | | | | - Abdol Ghaffar Ebadi
- Department of Agriculture, Jouybar Branch, Islamic Azad University, Jouybar, Iran
| | - Issa Amini
- Department of Chemistry, Payame Noor University, Tehran, Iran
| | - Esmail Vessally
- Department of Chemistry, Payame Noor University, Tehran, Iran
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4
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Mangialetto J, Gorissen K, Vermeersch L, Van Mele B, Van den Brande N, De Vleeschouwer F. Hydrogen-Bond-Assisted Diels–Alder Kinetics or Self-Healing in Reversible Polymer Networks? A Combined Experimental and Theoretical Study. Molecules 2022; 27:molecules27061961. [PMID: 35335324 PMCID: PMC8951177 DOI: 10.3390/molecules27061961] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Revised: 03/07/2022] [Accepted: 03/14/2022] [Indexed: 12/10/2022] Open
Abstract
Diels–Alder (DA) cycloadditions in reversible polymer networks are important for designing sustainable materials with self-healing properties. In this study, the DA kinetics of hydroxyl-substituted bis- and tetrafunctional furans with bis- and tris-functional maleimides, both containing ether-functionalized spacers, is investigated by modelling two equilibria representing the endo and exo cycloadduct formation. Concretely, the potential catalysis of the DA reaction through hydrogen bonding between hydroxyl of the furans and carbonyl of the maleimides or ether of the spacers is experimentally and theoretically scrutinized. Initial reaction rates and forward DA rate constants are determined by microcalorimetry at 20 °C for a model series of reversible networks, extended with (i) a hydroxyl-free network and hydroxyl-free linear or branched systems, and (ii) polypropylene glycol additives, increasing the hydroxyl concentration. A computational density-functional theory study is carried out on the endo and exo cycloadditions of furan and maleimide derivatives, representative for the experimental ones, in the absence and presence of ethylene glycol as additive. Additionally, an ester-substituted furan was investigated as a hydroxyl-free system for comparison. Experiment and theory indicate that the catalytic effect of H-bonding is absent or very limited. While increased concentration of H-bonding could in theory catalyze the DA reaction, the experimental results rule out this supposition.
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Affiliation(s)
- Jessica Mangialetto
- Physical Chemistry and Polymer Science (FYSC), Vrije Universiteit Brussel (VUB), Pleinlaan 2, 1050 Brussels, Belgium; (J.M.); (B.V.M.); (N.V.d.B.)
| | - Kiano Gorissen
- General Chemistry–Algemene Chemie (ALGC), Vrije Universiteit Brussel (VUB), Pleinlaan 2, 1050 Brussels, Belgium; (K.G.); (L.V.)
| | - Lise Vermeersch
- General Chemistry–Algemene Chemie (ALGC), Vrije Universiteit Brussel (VUB), Pleinlaan 2, 1050 Brussels, Belgium; (K.G.); (L.V.)
| | - Bruno Van Mele
- Physical Chemistry and Polymer Science (FYSC), Vrije Universiteit Brussel (VUB), Pleinlaan 2, 1050 Brussels, Belgium; (J.M.); (B.V.M.); (N.V.d.B.)
| | - Niko Van den Brande
- Physical Chemistry and Polymer Science (FYSC), Vrije Universiteit Brussel (VUB), Pleinlaan 2, 1050 Brussels, Belgium; (J.M.); (B.V.M.); (N.V.d.B.)
| | - Freija De Vleeschouwer
- General Chemistry–Algemene Chemie (ALGC), Vrije Universiteit Brussel (VUB), Pleinlaan 2, 1050 Brussels, Belgium; (K.G.); (L.V.)
- Correspondence:
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5
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Mueller E, Poulin I, Bodnaryk WJ, Hoare T. Click Chemistry Hydrogels for Extrusion Bioprinting: Progress, Challenges, and Opportunities. Biomacromolecules 2022; 23:619-640. [PMID: 34989569 DOI: 10.1021/acs.biomac.1c01105] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The emergence of 3D bioprinting has allowed a variety of hydrogel-based "bioinks" to be printed in the presence of cells to create precisely defined cell-loaded 3D scaffolds in a single step for advancing tissue engineering and/or regenerative medicine. While existing bioinks based primarily on ionic cross-linking, photo-cross-linking, or thermogelation have significantly advanced the field, they offer technical limitations in terms of the mechanics, degradation rates, and the cell viabilities achievable with the printed scaffolds, particularly in terms of aiming to match the wide range of mechanics and cellular microenvironments. Click chemistry offers an appealing solution to this challenge given that proper selection of the chemistry can enable precise tuning of both the gelation rate and the degradation rate, both key to successful tissue regeneration; simultaneously, the often bio-orthogonal nature of click chemistry is beneficial to maintain high cell viabilities within the scaffolds. However, to date, relatively few examples of 3D-printed click chemistry hydrogels have been reported, mostly due to the technical challenges of controlling mixing during the printing process to generate high-fidelity prints without clogging the printer. This review aims to showcase existing cross-linking modalities, characterize the advantages and disadvantages of different click chemistries reported, highlight current examples of click chemistry hydrogel bioinks, and discuss the design of mixing strategies to enable effective 3D extrusion bioprinting of click hydrogels.
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Affiliation(s)
- Eva Mueller
- Department of Chemical Engineering, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4L7, Canada
| | - Isabelle Poulin
- Department of Chemical Engineering, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4L7, Canada
| | - William James Bodnaryk
- Department of Chemical Engineering, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4L7, Canada
| | - Todd Hoare
- Department of Chemical Engineering, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4L7, Canada
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6
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Zhou Q, Sang Z, Rajagopalan KK, Sliozberg Y, Gardea F, Sukhishvili SA. Thermodynamics and Stereochemistry of Diels–Alder Polymer Networks: Role of Crosslinker Flexibility and Crosslinking Density. Macromolecules 2021. [DOI: 10.1021/acs.macromol.1c01662] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Qing Zhou
- Department of Materials Science & Engineering, Texas A&M University, College Station, Texas 77843, United States
| | - Zhen Sang
- Department of Materials Science & Engineering, Texas A&M University, College Station, Texas 77843, United States
| | - Kartik Kumar Rajagopalan
- Department of Materials Science & Engineering, Texas A&M University, College Station, Texas 77843, United States
| | - Yelena Sliozberg
- Weapons and Materials Research Directorate, DEVCOM Army Research Laboratory, Aberdeen Proving Ground, Maryland 21005, United States
| | - Frank Gardea
- Weapons and Materials Research Directorate, DEVCOM Army Research Laboratory South, College Station, Texas 77843, United States
| | - Svetlana A. Sukhishvili
- Department of Materials Science & Engineering, Texas A&M University, College Station, Texas 77843, United States
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7
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Hallooman D, Rhyman L, Dalkılıç E, Daştan A, Elzagheid MI, Domingo LR, Ramasami P. Theoretical Studies on the Mechanism of the Formation of Cyclopentadienes and Dihydropyridazines. ChemistrySelect 2021. [DOI: 10.1002/slct.202102928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Dhanashree Hallooman
- Computational Chemistry Group Department of Chemistry Faculty of Science University of Mauritius Moka, Réduit 80837 Mauritius
| | - Lydia Rhyman
- Computational Chemistry Group Department of Chemistry Faculty of Science University of Mauritius Moka, Réduit 80837 Mauritius
- Centre for Natural Product Research Department of Chemical Sciences University of Johannesburg, Doornfontein Johannesburg 2028 South Africa
| | - Erdin Dalkılıç
- Atatürk University Science Faculty, Department of Chemistry Erzurum 25240 Turkey
| | - Arif Daştan
- Atatürk University Science Faculty, Department of Chemistry Erzurum 25240 Turkey
| | - Mohamed I. Elzagheid
- Department of Chemical and Process Engineering Jubail Industrial College Jubail Industrial City 31961 Saudi Arabia
| | - Luis R. Domingo
- Department of Organic Chemistry University of Valencia Dr. Moliner 50 E-46100 Burjassot Valencia Spain
| | - Ponnadurai Ramasami
- Computational Chemistry Group Department of Chemistry Faculty of Science University of Mauritius Moka, Réduit 80837 Mauritius
- Centre for Natural Product Research Department of Chemical Sciences University of Johannesburg, Doornfontein Johannesburg 2028 South Africa
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8
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Dyan OT, Andreev RV, Zaikin PA. Substituents effects in the Diels-Alder reaction of 1,1-difluoronaphthalen-2(1H)-ones with cyclopentadiene. J Fluor Chem 2021. [DOI: 10.1016/j.jfluchem.2021.109859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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9
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Rizwan M, Baker AEG, Shoichet MS. Designing Hydrogels for 3D Cell Culture Using Dynamic Covalent Crosslinking. Adv Healthc Mater 2021; 10:e2100234. [PMID: 33987970 DOI: 10.1002/adhm.202100234] [Citation(s) in RCA: 74] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 04/22/2021] [Indexed: 12/17/2022]
Abstract
Designing simple biomaterials to replicate the biochemical and mechanical properties of tissues is an ongoing challenge in tissue engineering. For several decades, new biomaterials have been engineered using cytocompatible chemical reactions and spontaneous ligations via click chemistries to generate scaffolds and water swollen polymer networks, known as hydrogels, with tunable properties. However, most of these materials are static in nature, providing only macroscopic tunability of the scaffold mechanics, and do not reflect the dynamic environment of natural extracellular microenvironment. For more complex applications such as organoids or co-culture systems, there remain opportunities to investigate cells that locally remodel and change the physicochemical properties within the matrices. In this review, advanced biomaterials where dynamic covalent chemistry is used to produce stable 3D cell culture models and high-resolution constructs for both in vitro and in vivo applications, are discussed. The implications of dynamic covalent chemistry on viscoelastic properties of in vitro models are summarized, case studies in 3D cell culture are critically analyzed, and opportunities to further improve the performance of biomaterials for 3D tissue engineering are discussed.
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Affiliation(s)
- Muhammad Rizwan
- Department of Chemical Engineering and Applied Chemistry University of Toronto Toronto Ontario M5S 3E5 Canada
- Institute of Biomedical Engineering University of Toronto Toronto Ontario M5S 3G9 Canada
- Donnelly Centre for Cellular and Biomolecular Research University of Toronto Toronto Ontario M5S 3E1 Canada
| | - Alexander E. G. Baker
- Department of Chemical Engineering and Applied Chemistry University of Toronto Toronto Ontario M5S 3E5 Canada
- Institute of Biomedical Engineering University of Toronto Toronto Ontario M5S 3G9 Canada
- Donnelly Centre for Cellular and Biomolecular Research University of Toronto Toronto Ontario M5S 3E1 Canada
| | - Molly S. Shoichet
- Department of Chemical Engineering and Applied Chemistry University of Toronto Toronto Ontario M5S 3E5 Canada
- Institute of Biomedical Engineering University of Toronto Toronto Ontario M5S 3G9 Canada
- Donnelly Centre for Cellular and Biomolecular Research University of Toronto Toronto Ontario M5S 3E1 Canada
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10
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Jana K, Wakchaure PD, Hussain N, Mukherjee D, Ganguly B. The mechanism of conversion of substituted glycals to chiral acenes via Diels-Alder reaction: a computational study. Org Biomol Chem 2021; 19:6353-6367. [PMID: 34231642 DOI: 10.1039/d1ob00408e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Synthesis of linearly fused aromatic systems using a glycal-based diene with an aryne is a long-standing topic of interest in glycal chemistry. We have examined the mechanistic pathways for the transformation of substituted glycals to chiral fused aromatic cores via Diels-Alder (DA) reaction using the SMDACN-M06-2X/6-31G(d) level of theory. The DA reactions of E (1a) and Z (1a') forms of C-2 alkenyl glycal and an aryl glycal (1b) as a diene were examined with a benzyne intermediate generated as a dienophile. The computational results reveal that 1a and 1b can only be transformed into the fused aromatic cores by the base-catalyzed reaction because a [1,5] sigmatropic hydrogen shift is not feasible. The activation free energy barrier for the base-catalyzed proton abstraction process is 4.2 kcal mol-1 and there is almost no barrier for stereoisomeric 1a DA-complexes. The activation free energy barrier values for stereoisomeric 1b DA-complexes for the base-catalyzed proton abstraction process are 10.8 and 12.4 kcal mol-1. The appropriate orientation of glycal-ring-oxygen and hydrogen at the 5th position of Z (1a') forms of C-2 alkenyl glycal facilitates the [1,5] sigmatropic hydrogen shift; however, the base-catalyzed reaction is energetically more favored than the former case. The rate-determining step for 1a and 1a' is the ring-opening step (18.2 and 19.5 kcal mol-1 for the S-stereoisomer), whereas the DA adduct formation step is the rate-determining step for 1b (16.1 kcal mol-1 for the S-stereoisomer). The structural analysis reveals the formation of the preferred S-stereoisomer over the R-stereoisomer with the respective dienes.
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Affiliation(s)
- Kalyanashis Jana
- CSIR-Central Salt and Marine Chemicals Research Institute, Bhavnagar 364002, India. and Academy of Scientific and Innovative Research, Ghaziabad, Uttar Pradesh-201 002, India
| | - Padmaja D Wakchaure
- CSIR-Central Salt and Marine Chemicals Research Institute, Bhavnagar 364002, India. and Academy of Scientific and Innovative Research, Ghaziabad, Uttar Pradesh-201 002, India
| | - Nazar Hussain
- Academy of Scientific and Innovative Research, Ghaziabad, Uttar Pradesh-201 002, India and Natural Product Chemistry Division, Indian Institute of Integrative Medicine (IIIM), Jammu 180001, India
| | - Debaraj Mukherjee
- Academy of Scientific and Innovative Research, Ghaziabad, Uttar Pradesh-201 002, India and Natural Product Chemistry Division, Indian Institute of Integrative Medicine (IIIM), Jammu 180001, India
| | - Bishwajit Ganguly
- CSIR-Central Salt and Marine Chemicals Research Institute, Bhavnagar 364002, India. and Academy of Scientific and Innovative Research, Ghaziabad, Uttar Pradesh-201 002, India
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Lossouarn A, Renard PY, Sabot C. Tailored Bioorthogonal and Bioconjugate Chemistry: A Source of Inspiration for Developing Kinetic Target-Guided Synthesis Strategies. Bioconjug Chem 2020; 32:63-72. [PMID: 33232599 DOI: 10.1021/acs.bioconjchem.0c00568] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Kinetic target-guided synthesis (KTGS) is a promising tool for the discovery of biologically active compounds. It relies on the identification of potent ligands that are covalently assembled by the biological targets themselves from a pool of reagents. Significant effort is devoted to developing new KTGS strategies; however, only a handful of biocompatible reactions are available, which may be insufficient to meet the specificities (stability, dynamics, active site topology, etc.) of a wide range of biological targets with therapeutic potential. This Topical Review proposes a retrospective analysis of existing KTGS ligation tools, in terms of their kinetics and analogy with other biocompatible reactions, and provides new clues to expand the KTGS toolkit. By way of examples, a nonexhaustive selection of such chemical ligation tools belonging to different classes of reactions as promising candidate reactions for KTGS are suggested.
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Affiliation(s)
- Alexis Lossouarn
- Normandie Université, Centre National de la Recherche Scientifique, UNIROUEN, INSA Rouen, COBRA, UMR 6014 & FR 3038, 76000, Rouen, France
| | - Pierre-Yves Renard
- Normandie Université, Centre National de la Recherche Scientifique, UNIROUEN, INSA Rouen, COBRA, UMR 6014 & FR 3038, 76000, Rouen, France
| | - Cyrille Sabot
- Normandie Université, Centre National de la Recherche Scientifique, UNIROUEN, INSA Rouen, COBRA, UMR 6014 & FR 3038, 76000, Rouen, France
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12
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Accurate Diels-Alder Energies and Endo Selectivity in Ionic Liquids Using the OPLS-VSIL Force Field. Int J Mol Sci 2020; 21:ijms21041190. [PMID: 32054023 PMCID: PMC7072795 DOI: 10.3390/ijms21041190] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 02/06/2020] [Accepted: 02/08/2020] [Indexed: 01/17/2023] Open
Abstract
Our recently developed optimized potentials for liquid simulations-virtual site ionic liquid (OPLS-VSIL) force field has been shown to provide accurate bulk phase properties and local ion-ion interactions for a wide variety of imidazolium-based ionic liquids. The force field features a virtual site that offloads negative charge to inside the plane of the ring with careful attention given to hydrogen bonding interactions. In this study, the Diels-Alder reaction between cyclopentadiene and methyl acrylate was computationally investigated in the ionic liquid 1-butyl-3-methylimidazolium hexafluorophosphate, [BMIM][PF6], as a basis for the validation of the OPLS-VSIL to properly reproduce a reaction medium environment. Mixed ab initio quantum mechanics and molecular mechanics (QM/MM) calculations coupled to free energy perturbation and Monte Carlo sampling (FEP/MC) that utilized M06-2X/6-31G(d) and OPLS-VSIL gave activation free energy barriers of 14.9 and 16.0 kcal/mol for the endo-cis and exo-cis Diels-Alder reaction pathways, respectively (exptl. ΔH‡ of 14.6 kcal/mol). The endo selectivity trend was correctly predicted with a calculated 73% endo preference. The rate and selectivity enhancements present in the endo conformation were found to arise from preferential hydrogen bonding with the exposed C4 ring hydrogen on the BMIM cation. Weaker electronic stabilization of the exo transition state was predicted. For comparison, our earlier ±0.8 charge-scaled OPLS-2009IL force field also yielded a ΔG‡ of 14.9 kcal/mol for the favorable endo reaction pathway but did not adequately capture the highly organized solvent interactions present between the cation and Diels-Alder transition state.
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13
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Lossouarn A, Renault K, Bailly L, Frisby A, Le Nahenec-Martel P, Renard PY, Sabot C. Maleimide-based metal-free ligation with dienes: a comparative study. Org Biomol Chem 2020; 18:3874-3887. [DOI: 10.1039/d0ob00403k] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Maleimide-based Diels–Alder strategies for bioconjugation are compared in terms of dienes accessibility and stability, reactions rates, as well as products isolation and stability.
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Affiliation(s)
| | | | | | - Axel Frisby
- Normandie Univ
- CNRS
- UNIROUEN
- INSA Rouen
- 76000 Rouen
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14
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Developing non-linear rate constant QSPR using decision trees and multi-gene genetic programming. Comput Chem Eng 2019. [DOI: 10.1016/j.compchemeng.2019.05.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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15
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Mondal P, Jana G, Behera PK, Chattaraj PK, Singha NK. A new healable polymer material based on ultrafast Diels–Alder ‘click’ chemistry using triazolinedione and fluorescent anthracyl derivatives: a mechanistic approach. Polym Chem 2019. [DOI: 10.1039/c9py00499h] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Development of a new healable polymer based on ultrafast Diels–Alder ‘click’ chemistry using fluorescent anthracyl and TAD derivatives. The ultrafast mechanistic approach is rationalized via Density Functional Theory (DFT) study.
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Affiliation(s)
- Prantik Mondal
- Rubber Technology Centre
- Indian Institute of Technology Kharagpur
- India
| | - Gourhari Jana
- Department of Chemistry
- Indian Institute of Technology Kharagpur
- India
| | | | - Pratim Kumar Chattaraj
- Department of Chemistry
- Indian Institute of Technology Kharagpur
- India
- Department of Chemistry
- Indian Institute of Technology Bombay
| | - Nikhil K. Singha
- Rubber Technology Centre
- Indian Institute of Technology Kharagpur
- India
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16
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Taimoory SM, Sadraei SI, Fayoumi RA, Nasri S, Revington M, Trant JF. Preparation and Characterization of a Small Library of Thermally-Labile End-Caps for Variable-Temperature Triggering of Self-Immolative Polymers. J Org Chem 2018; 83:4427-4440. [PMID: 29589930 DOI: 10.1021/acs.joc.8b00135] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The reaction between furans and maleimides has increasingly become a method of interest as its reversibility makes it a useful tool for applications ranging from self-healing materials, to self-immolative polymers, to hydrogels for cell culture and for the preparation of bone repair. However, most of these applications have relied on simple monosubstituted furans and simple maleimides and have not extensively evaluated the potential thermal variability inherent in the process that is achievable through simple substrate modification. A small library of cycloadducts suitable for the above applications was prepared, and the temperature dependence of the retro-Diels-Alder processes was determined through in situ 1H NMR analyses complemented by computational calculations. The practical range of the reported systems ranges from 40 to >110 °C. The cycloreversion reactions are more complex than would be expected based on simple trends expected based on frontier molecular orbital analyses of the materials.
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Affiliation(s)
- S Maryamdokht Taimoory
- Department of Chemistry and Biochemistry , University of Windsor , 401 Sunset Avenue , Windsor , Ontario N9B 3P4 , Canada
| | - S Iraj Sadraei
- Department of Chemistry and Biochemistry , University of Windsor , 401 Sunset Avenue , Windsor , Ontario N9B 3P4 , Canada
| | - Rose Anne Fayoumi
- Department of Chemistry and Biochemistry , University of Windsor , 401 Sunset Avenue , Windsor , Ontario N9B 3P4 , Canada
| | - Sarah Nasri
- Department of Chemistry and Biochemistry , University of Windsor , 401 Sunset Avenue , Windsor , Ontario N9B 3P4 , Canada
| | - Matthew Revington
- Department of Chemistry and Biochemistry , University of Windsor , 401 Sunset Avenue , Windsor , Ontario N9B 3P4 , Canada
| | - John F Trant
- Department of Chemistry and Biochemistry , University of Windsor , 401 Sunset Avenue , Windsor , Ontario N9B 3P4 , Canada.,Canadian Centre for Alternatives to Animal Methods , University of Windsor , 401 Sunset Avenue , Windsor , Ontario N9B 3P4 , Canada
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17
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Datta S, Dev VA, Eden MR. Hybrid genetic algorithm-decision tree approach for rate constant prediction using structures of reactants and solvent for Diels-Alder reaction. Comput Chem Eng 2017. [DOI: 10.1016/j.compchemeng.2017.02.022] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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18
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Rivero U, Meuwly M, Willitsch S. A computational study of the Diels-Alder reactions between 2,3-dibromo-1,3-butadiene and maleic anhydride. Chem Phys Lett 2017. [DOI: 10.1016/j.cplett.2017.03.063] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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19
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Zaikin PA, Dyan OT, Fadeev DS, Gatilov YV, Borodkin GI. 1,1-Difluoronaphthalene-2(1 H )-ones in Diels-Alder reaction. J Fluor Chem 2017. [DOI: 10.1016/j.jfluchem.2017.04.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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20
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Abstract
We recently showed for a large data set of pKas and reduction potentials that free energies calculated directly within the SMD continuum model compares very well with corresponding thermodynamic cycle calculations in both aqueous and organic solvents [ Phys. Chem. Chem. Phys. 2015 , 17 , 2859 ]. In this paper, we significantly expand the scope of our study to examine the suitability of this approach for calculating general solution phase kinetics and thermodynamics, in conjunction with several commonly used solvation models (SMD-M062X, SMD-HF, CPCM-UAKS, and CPCM-UAHF) for a broad range of systems. This includes cluster-continuum schemes for pKa calculations as well as various neutral, radical, and ionic reactions such as enolization, cycloaddition, hydrogen and chlorine atom transfer, and SN2 and E2 reactions. On the basis of this benchmarking study, we conclude that the accuracies of both approaches are generally very similar-the mean errors for Gibbs free energy changes of neutral and ionic reactions are approximately 5 and 25 kJ mol(-1), respectively. In systems where there are significant structural changes due to solvation, as is the case for certain ionic transition states and amino acids, the direct approach generally afford free energy changes that are in better agreement with experiment.
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Affiliation(s)
- Junming Ho
- Agency for Science, Technology and Research, Institute of High Performance Computing , 1 Fusionopolis Way, #16-16 Connexis, Singapore 138632.,Department of Chemistry, Yale University , P.O. Box 208107, New Haven, Connecticut 06520, United States
| | - Mehmed Z Ertem
- Chemistry Department, Brookhaven National Laboratory , Upton, New York 11973, United States
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21
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Weissman MR, Winger KT, Ghiassian S, Gobbo P, Workentin MS. Insights on the Application of the Retro Michael-Type Addition on Maleimide-Functionalized Gold Nanoparticles in Biology and Nanomedicine. Bioconjug Chem 2016; 27:586-93. [DOI: 10.1021/acs.bioconjchem.5b00600] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Max R. Weissman
- The University of Western Ontario and the Centre for Materials and Biomaterials Research, Richmond Street, London, Ontario N6A 5B7, Canada
| | - Kathleen T. Winger
- The University of Western Ontario and the Centre for Materials and Biomaterials Research, Richmond Street, London, Ontario N6A 5B7, Canada
| | - Sara Ghiassian
- The University of Western Ontario and the Centre for Materials and Biomaterials Research, Richmond Street, London, Ontario N6A 5B7, Canada
| | - Pierangelo Gobbo
- The University of Western Ontario and the Centre for Materials and Biomaterials Research, Richmond Street, London, Ontario N6A 5B7, Canada
| | - Mark S. Workentin
- The University of Western Ontario and the Centre for Materials and Biomaterials Research, Richmond Street, London, Ontario N6A 5B7, Canada
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22
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Sheena Mary Y, Aswathy VV, Panicker CY, Bielenica A, Brzózka P, Savczenko O, Armaković S, Armaković SJ, Van Alsenoy C. Spectroscopic, single crystal XRD structure, DFT and molecular dynamics investigation of 1-(3-chloro-4-fluorophenyl)-3-[3-(trifluoromethyl)phenyl]thiourea. RSC Adv 2016. [DOI: 10.1039/c6ra21396k] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The title compound 1-(3-chloro-4-fluorophenyl)-3-[3-(trifluoromethyl) phenyl]thiourea (ANF-2) was synthesized and structurally characterized by single crystal XRD.
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Affiliation(s)
- Y. Sheena Mary
- Department of Physics
- Fatima Mata National College
- Kollam
- India
| | - V. V. Aswathy
- Department of Physics
- Fatima Mata National College
- Kollam
- India
| | | | - Anna Bielenica
- Chair and Department of Biochemistry
- Medical University of Warsaw
- 02-097 Warszawa
- Poland
| | - Paulina Brzózka
- Department of Inorganic and Analytical Chemistry
- Faculty of Pharmacy
- Medical University of Warsaw
- 02-097 Warszawa
- Poland
| | | | - Stevan Armaković
- University of Novi Sad
- Faculty of Sciences
- Department of Physics
- 21000 Novi Sad
- Serbia
| | - Sanja J. Armaković
- University of Novi Sad
- Faculty of Sciences
- Department of Chemistry
- Biochemistry and Environmental Protection
- 21000 Novi Sad
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23
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The Diels–Alder reaction: A powerful tool for the design of drug delivery systems and biomaterials. Eur J Pharm Biopharm 2015; 97:438-53. [DOI: 10.1016/j.ejpb.2015.06.007] [Citation(s) in RCA: 114] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2015] [Revised: 06/03/2015] [Accepted: 06/05/2015] [Indexed: 01/06/2023]
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24
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He CQ, Chen TQ, Patel A, Karabiyikoglu S, Merlic CA, Houk KN. Distortion, Tether, and Entropy Effects on Transannular Diels–Alder Cycloaddition Reactions of 10–18-Membered Rings. J Org Chem 2015; 80:11039-47. [DOI: 10.1021/acs.joc.5b02288] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Cyndi Qixin He
- Department of Chemistry and Biochemistry and ‡Department of Chemical and Biochemical
Engineering, University of California, Los Angeles, California 90095, United States
| | - Tiffany Q. Chen
- Department of Chemistry and Biochemistry and ‡Department of Chemical and Biochemical
Engineering, University of California, Los Angeles, California 90095, United States
| | - Ashay Patel
- Department of Chemistry and Biochemistry and ‡Department of Chemical and Biochemical
Engineering, University of California, Los Angeles, California 90095, United States
| | - Sedef Karabiyikoglu
- Department of Chemistry and Biochemistry and ‡Department of Chemical and Biochemical
Engineering, University of California, Los Angeles, California 90095, United States
| | - Craig A. Merlic
- Department of Chemistry and Biochemistry and ‡Department of Chemical and Biochemical
Engineering, University of California, Los Angeles, California 90095, United States
| | - K. N. Houk
- Department of Chemistry and Biochemistry and ‡Department of Chemical and Biochemical
Engineering, University of California, Los Angeles, California 90095, United States
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25
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Abstract
The first total synthesis of rottlerin is described. The methodology allows the development of potential novel protein kinase C δ (PKCδ) analogues for better treatment of various diseases. Kamalachalcone A and dimeric rottlerin were synthesized in a very practical and economical way using FeCl3 as a catalyst.
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Affiliation(s)
- Kenneth K C Hong
- School of Chemistry, The University of New South Wales , Sydney, New South Wales 2052, Australia
| | - Graham E Ball
- School of Chemistry, The University of New South Wales , Sydney, New South Wales 2052, Australia
| | - David StC Black
- School of Chemistry, The University of New South Wales , Sydney, New South Wales 2052, Australia
| | - Naresh Kumar
- School of Chemistry, The University of New South Wales , Sydney, New South Wales 2052, Australia
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26
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Ghiassian S, Gobbo P, Workentin MS. Water-Soluble Maleimide-Modified Gold Nanoparticles (AuNPs) as a Platform for Cycloaddition Reactions. European J Org Chem 2015. [DOI: 10.1002/ejoc.201500685] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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27
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Kirchhof S, Strasser A, Wittmann HJ, Messmann V, Hammer N, Goepferich AM, Brandl FP. New insights into the cross-linking and degradation mechanism of Diels–Alder hydrogels. J Mater Chem B 2015; 3:449-457. [DOI: 10.1039/c4tb01680g] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Degradation of Diels–Alder hydrogels occurs by retro-Diels–Alder reaction followed by OH−-catalyzed ring-opening hydrolysis of maleimide groups to unreactive maleamic acid derivatives.
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Affiliation(s)
- Susanne Kirchhof
- Department of Pharmaceutical Technology
- Faculty of Chemistry and Pharmacy
- University of Regensburg
- 93040 Regensburg
- Germany
| | - Andrea Strasser
- Department of Pharmaceutical and Medicinal Chemistry II
- Faculty of Chemistry and Pharmacy
- University of Regensburg
- 93040 Regensburg
- Germany
| | - Hans-Joachim Wittmann
- Department of Pharmaceutical and Medicinal Chemistry II
- Faculty of Chemistry and Pharmacy
- University of Regensburg
- 93040 Regensburg
- Germany
| | - Viktoria Messmann
- Department of Pharmaceutical Technology
- Faculty of Chemistry and Pharmacy
- University of Regensburg
- 93040 Regensburg
- Germany
| | - Nadine Hammer
- Department of Pharmaceutical Technology
- Faculty of Chemistry and Pharmacy
- University of Regensburg
- 93040 Regensburg
- Germany
| | - Achim M. Goepferich
- Department of Pharmaceutical Technology
- Faculty of Chemistry and Pharmacy
- University of Regensburg
- 93040 Regensburg
- Germany
| | - Ferdinand P. Brandl
- Department of Pharmaceutical Technology
- Faculty of Chemistry and Pharmacy
- University of Regensburg
- 93040 Regensburg
- Germany
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28
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Sun Z, Wang Q, Xu Y, Wang Z. A computationally designed titanium-mediated amination of allylic alcohols for the synthesis of secondary allylamines. RSC Adv 2015. [DOI: 10.1039/c5ra18503c] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
A direct amination on allylic alcohols under mild conditions was enlightened by computational investigations and implemented in secondary allylamines synthesis.
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Affiliation(s)
- Zunming Sun
- State Key Laboratory and Institute of Elemento-Organic Chemistry
- Nankai University
- Tianjin 300071
- China
| | - Qingxia Wang
- State Key Laboratory and Institute of Elemento-Organic Chemistry
- Nankai University
- Tianjin 300071
- China
| | - Yi Xu
- State Key Laboratory and Institute of Elemento-Organic Chemistry
- Nankai University
- Tianjin 300071
- China
| | - Zhihong Wang
- State Key Laboratory and Institute of Elemento-Organic Chemistry
- Nankai University
- Tianjin 300071
- China
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29
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Hammer N, Brandl FP, Kirchhof S, Messmann V, Goepferich AM. Protein Compatibility of Selected Cross-linking Reactions for Hydrogels. Macromol Biosci 2014; 15:405-13. [DOI: 10.1002/mabi.201400379] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2014] [Revised: 10/14/2014] [Indexed: 01/18/2023]
Affiliation(s)
- Nadine Hammer
- Department of Pharmaceutical Technology, Faculty of Chemistry and Pharmacy; University of Regensburg; Universitätsstr. 31 93040 Regensburg Germany
| | - Ferdinand P. Brandl
- Department of Pharmaceutical Technology, Faculty of Chemistry and Pharmacy; University of Regensburg; Universitätsstr. 31 93040 Regensburg Germany
| | - Susanne Kirchhof
- Department of Pharmaceutical Technology, Faculty of Chemistry and Pharmacy; University of Regensburg; Universitätsstr. 31 93040 Regensburg Germany
| | - Viktoria Messmann
- Department of Pharmaceutical Technology, Faculty of Chemistry and Pharmacy; University of Regensburg; Universitätsstr. 31 93040 Regensburg Germany
| | - Achim M. Goepferich
- Department of Pharmaceutical Technology, Faculty of Chemistry and Pharmacy; University of Regensburg; Universitätsstr. 31 93040 Regensburg Germany
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30
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Solid-phase crystallization of spray-dried glucose powders: A perspective and comparison with lactose and sucrose. ADV POWDER TECHNOL 2014. [DOI: 10.1016/j.apt.2014.06.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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31
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L. Schwan A, Gh. Shkoor M, Nikoloska I. Introducing the Diels-Alder Reactivity of 2-Furanmethanethiol with Selected Maleic Acid Derivatives. HETEROCYCLES 2014. [DOI: 10.3987/com-13-s(s)112] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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32
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Quantitative structure-activation barrier relationship modeling for Diels-Alder ligations utilizing quantum chemical structural descriptors. Chem Cent J 2013; 7:171. [PMID: 24171724 PMCID: PMC4176756 DOI: 10.1186/1752-153x-7-171] [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: 07/24/2013] [Accepted: 10/23/2013] [Indexed: 11/22/2022] Open
Abstract
Background In the present study, we show the correlation of quantum chemical structural descriptors with the activation barriers of the Diels-Alder ligations. A set of 72 non-catalysed Diels-Alder reactions were subjected to quantitative structure-activation barrier relationship (QSABR) under the framework of theoretical quantum chemical descriptors calculated solely from the structures of diene and dienophile reactants. Experimental activation barrier data were obtained from literature. Descriptors were computed using Hartree-Fock theory using 6-31G(d) basis set as implemented in Gaussian 09 software. Results Variable selection and model development were carried out by stepwise multiple linear regression methodology. Predictive performance of the quantitative structure-activation barrier relationship (QSABR) model was assessed by training and test set concept and by calculating leave-one-out cross-validated Q2 and predictive R2 values. The QSABR model can explain and predict 86.5% and 80% of the variances, respectively, in the activation energy barrier training data. Alternatively, a neural network model based on back propagation of errors was developed to assess the nonlinearity of the sought correlations between theoretical descriptors and experimental reaction barriers. Conclusions A reasonable predictability for the activation barrier of the test set reactions was obtained, which enabled an exploration and interpretation of the significant variables responsible for Diels-Alder interaction between dienes and dienophiles. Thus, studies in the direction of QSABR modelling that provide efficient and fast prediction of activation barriers of the Diels-Alder reactions turn out to be a meaningful alternative to transition state theory based computation.
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33
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Volp KA, Harned AM. Origin of Stereoselectivity of the Alkylation of Cyclohexadienone-Derived Bicyclic Malonates. J Org Chem 2013; 78:7554-64. [DOI: 10.1021/jo4011238] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Kelly A. Volp
- Department of Chemistry, University of Minnesota—Twin Cities, 207 Pleasant St. SE, Minneapolis, Minnesota
55455, United States
| | - Andrew M. Harned
- Department of Chemistry, University of Minnesota—Twin Cities, 207 Pleasant St. SE, Minneapolis, Minnesota
55455, United States
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34
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Linder M, Brinck T. On the method-dependence of transition state asynchronicity in Diels–Alder reactions. Phys Chem Chem Phys 2013; 15:5108-14. [DOI: 10.1039/c3cp44319a] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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35
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Prathyusha V, Priyakumar UD. Role of conformational properties on the transannular Diels–Alder reactivity of macrocyclic trienes with varying linker lengths. RSC Adv 2013. [DOI: 10.1039/c3ra42045k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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36
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Patterson DM, Nazarova LA, Xie B, Kamber DN, Prescher JA. Functionalized Cyclopropenes As Bioorthogonal Chemical Reporters. J Am Chem Soc 2012; 134:18638-43. [DOI: 10.1021/ja3060436] [Citation(s) in RCA: 269] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- David M. Patterson
- Departments
of Chemistry, ‡Molecular Biology and Biochemistry, and §Pharmaceutical Science, University of California - Irvine, Irvine,
California 92697, United States
| | - Lidia A. Nazarova
- Departments
of Chemistry, ‡Molecular Biology and Biochemistry, and §Pharmaceutical Science, University of California - Irvine, Irvine,
California 92697, United States
| | - Bryan Xie
- Departments
of Chemistry, ‡Molecular Biology and Biochemistry, and §Pharmaceutical Science, University of California - Irvine, Irvine,
California 92697, United States
| | - David N. Kamber
- Departments
of Chemistry, ‡Molecular Biology and Biochemistry, and §Pharmaceutical Science, University of California - Irvine, Irvine,
California 92697, United States
| | - Jennifer A. Prescher
- Departments
of Chemistry, ‡Molecular Biology and Biochemistry, and §Pharmaceutical Science, University of California - Irvine, Irvine,
California 92697, United States
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37
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Linder M, Brinck T. Stepwise Diels-Alder: more than just an oddity? A computational mechanistic study. J Org Chem 2012; 77:6563-73. [PMID: 22780581 DOI: 10.1021/jo301176t] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
We have employed hybrid DFT and SCS-MP2 calculations at the SMD-PCM-6-311++G(2d,2p)//6-31+G(d) level to investigate the relationship between three possible channels for forming a Diels-Alder adduct from a highly nucleophilic diene and moderately to highly electrophilic dienophiles. We discuss geometries optimized using the B3LYP and M06-2X functionals with the 6-31+(d) basis set. The transition states and intermediates are characterized on the basis of geometric and electronic properties, and we also address the possibility of predicting detectability of a zwitterionic intermediate based on its relative stability. Our results show that a conventional Diels-Alder transition state conformation yields intermediates in all four investigated cases, but that these are too short-lived to be detected experimentally for the less activated reactants. The stepwise trans pathway, beginning with a conjugate addition-like transition state, becomes increasingly competitive with more activated reactants and is indeed favored for the most electrophilic dienophiles. Addition of a trans diene leads to a dead-end as the trans intermediates have insurmountable rotation barriers that prohibit formation of the second bond, unless another, heterocyclic intermediate is formed. We also show that introduction of a hydrogen bond donating catalyst favors a stepwise pathway even for less activated dienophiles.
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Affiliation(s)
- Mats Linder
- Applied Physical Chemistry, KTH Royal Institute of Technology, Teknikringen 30, S-100 44 Stockholm
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