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Shyshov O, Brachvogel R, Bachmann T, Srikantharajah R, Segets D, Hampel F, Puchta R, von Delius M. Adaptive Behavior of Dynamic Orthoester Cryptands. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201609855] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Oleksandr Shyshov
- Institute of Organic Chemistry and Advanced Materials University of Ulm Albert-Einstein-Allee 11 89081 Ulm Germany
| | - René‐Chris Brachvogel
- Institute of Organic Chemistry and Advanced Materials University of Ulm Albert-Einstein-Allee 11 89081 Ulm Germany
| | - Tobias Bachmann
- Department of Chemistry and Pharmacy, Institute of Organic Chemistry, and Computer Chemistry Center (CCC) Friedrich-Alexander Universität Erlangen-Nürnberg (FAU) Henkestrasse 42 91054 Erlangen Germany
| | - Rubitha Srikantharajah
- Institute of Particle Technology (LFG) and Interdisciplinary Center for Functional Particle Systems (FPS) Friedrich-Alexander Universität Erlangen-Nürnberg (FAU) Cauerstrasse 4 91058 Erlangen Germany
| | - Doris Segets
- Institute of Particle Technology (LFG) and Interdisciplinary Center for Functional Particle Systems (FPS) Friedrich-Alexander Universität Erlangen-Nürnberg (FAU) Cauerstrasse 4 91058 Erlangen Germany
| | - Frank Hampel
- Department of Chemistry and Pharmacy, Institute of Organic Chemistry, and Computer Chemistry Center (CCC) Friedrich-Alexander Universität Erlangen-Nürnberg (FAU) Henkestrasse 42 91054 Erlangen Germany
| | - Ralph Puchta
- Department of Chemistry and Pharmacy, Institute of Organic Chemistry, and Computer Chemistry Center (CCC) Friedrich-Alexander Universität Erlangen-Nürnberg (FAU) Henkestrasse 42 91054 Erlangen Germany
| | - Max von Delius
- Institute of Organic Chemistry and Advanced Materials University of Ulm Albert-Einstein-Allee 11 89081 Ulm Germany
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Shyshov O, Brachvogel R, Bachmann T, Srikantharajah R, Segets D, Hampel F, Puchta R, von Delius M. Adaptive Behavior of Dynamic Orthoester Cryptands. Angew Chem Int Ed Engl 2016; 56:776-781. [DOI: 10.1002/anie.201609855] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2016] [Revised: 11/22/2016] [Indexed: 11/11/2022]
Affiliation(s)
- Oleksandr Shyshov
- Institute of Organic Chemistry and Advanced Materials University of Ulm Albert-Einstein-Allee 11 89081 Ulm Germany
| | - René‐Chris Brachvogel
- Institute of Organic Chemistry and Advanced Materials University of Ulm Albert-Einstein-Allee 11 89081 Ulm Germany
| | - Tobias Bachmann
- Department of Chemistry and Pharmacy, Institute of Organic Chemistry, and Computer Chemistry Center (CCC) Friedrich-Alexander Universität Erlangen-Nürnberg (FAU) Henkestrasse 42 91054 Erlangen Germany
| | - Rubitha Srikantharajah
- Institute of Particle Technology (LFG) and Interdisciplinary Center for Functional Particle Systems (FPS) Friedrich-Alexander Universität Erlangen-Nürnberg (FAU) Cauerstrasse 4 91058 Erlangen Germany
| | - Doris Segets
- Institute of Particle Technology (LFG) and Interdisciplinary Center for Functional Particle Systems (FPS) Friedrich-Alexander Universität Erlangen-Nürnberg (FAU) Cauerstrasse 4 91058 Erlangen Germany
| | - Frank Hampel
- Department of Chemistry and Pharmacy, Institute of Organic Chemistry, and Computer Chemistry Center (CCC) Friedrich-Alexander Universität Erlangen-Nürnberg (FAU) Henkestrasse 42 91054 Erlangen Germany
| | - Ralph Puchta
- Department of Chemistry and Pharmacy, Institute of Organic Chemistry, and Computer Chemistry Center (CCC) Friedrich-Alexander Universität Erlangen-Nürnberg (FAU) Henkestrasse 42 91054 Erlangen Germany
| | - Max von Delius
- Institute of Organic Chemistry and Advanced Materials University of Ulm Albert-Einstein-Allee 11 89081 Ulm Germany
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Jadhav KB, Lichtenecker RJ, Bullach A, Mandal B, Arndt HD. Dynamic Combinatorial Enrichment of PolyconformationalD-/L-Peptide Dimers. Chemistry 2015; 21:5898-908. [DOI: 10.1002/chem.201405413] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Indexed: 01/19/2023]
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Matache M, Bogdan E, Hădade ND. Selective Host Molecules Obtained by Dynamic Adaptive Chemistry. Chemistry 2014; 20:2106-31. [DOI: 10.1002/chem.201303504] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Sakulsombat M, Zhang Y, Ramström O. Dynamic Asymmetric Hemithioacetal Transformation by Lipase-Catalyzed γ-Lactonization: In Situ Tandem Formation of 1,3-Oxathiolan-5-one Derivatives. Chemistry 2012; 18:6129-32. [DOI: 10.1002/chem.201102139] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2011] [Revised: 10/27/2011] [Indexed: 11/06/2022]
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Cougnon FBL, Jenkins NA, Pantoş GD, Sanders JKM. Templated Dynamic Synthesis of a [3]Catenane. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201106885] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Cougnon FBL, Jenkins NA, Pantoş GD, Sanders JKM. Templated Dynamic Synthesis of a [3]Catenane. Angew Chem Int Ed Engl 2011; 51:1443-7. [DOI: 10.1002/anie.201106885] [Citation(s) in RCA: 99] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2011] [Revised: 10/27/2011] [Indexed: 11/09/2022]
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Capela MDF, Mosey NJ, Xing L, Wang R, Petitjean A. Amine Exchange in Formamidines: An Experimental and Theoretical Study. Chemistry 2011; 17:4598-612. [DOI: 10.1002/chem.201002389] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2010] [Indexed: 11/05/2022]
Affiliation(s)
- Marinha dF. Capela
- Department of Chemistry, Queen's University, 90 Bader Lane, Kingston, ON K7 L 3N6 (Canada), Fax: (+1) 613‐533‐6669
| | - Nicholas J. Mosey
- Department of Chemistry, Queen's University, 90 Bader Lane, Kingston, ON K7 L 3N6 (Canada), Fax: (+1) 613‐533‐6669
| | - Liyan Xing
- Department of Chemistry, Queen's University, 90 Bader Lane, Kingston, ON K7 L 3N6 (Canada), Fax: (+1) 613‐533‐6669
| | - Ruiyao Wang
- Department of Chemistry, Queen's University, 90 Bader Lane, Kingston, ON K7 L 3N6 (Canada), Fax: (+1) 613‐533‐6669
| | - Anne Petitjean
- Department of Chemistry, Queen's University, 90 Bader Lane, Kingston, ON K7 L 3N6 (Canada), Fax: (+1) 613‐533‐6669
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Buchs née Levrand B, Godin G, Trachsel A, de Saint Laumer JY, Lehn JM, Herrmann A. Reversible Aminal Formation: Controlling the Evaporation of Bioactive Volatiles by Dynamic Combinatorial/Covalent Chemistry. European J Org Chem 2010. [DOI: 10.1002/ejoc.201001433] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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del Amo V, Philp D. Integrating Replication-Based Selection Strategies in Dynamic Covalent Systems. Chemistry 2010; 16:13304-18. [DOI: 10.1002/chem.201000423] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Caraballo R, Sakulsombat M, Ramström O. Towards Dynamic Drug Design: Identification and Optimization of β-Galactosidase Inhibitors from a Dynamic Hemithioacetal System. Chembiochem 2010; 11:1600-6. [DOI: 10.1002/cbic.201000158] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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Caraballo R, Dong H, Ribeiro JP, Jiménez-Barbero J, Ramström O. Direct STD NMR identification of beta-galactosidase inhibitors from a virtual dynamic hemithioacetal system. Angew Chem Int Ed Engl 2010; 49:589-93. [PMID: 20013972 DOI: 10.1002/anie.200903920] [Citation(s) in RCA: 93] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Rémi Caraballo
- Department of Chemistry, KTH-Royal Institute of Technology, Teknikringen 30, 10044 Stockholm, Sweden
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Di Stefano S. Theoretical features of macrocyclization equilibria and their application on transacetalation based dynamic libraries. J PHYS ORG CHEM 2010. [DOI: 10.1002/poc.1674] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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14
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Caraballo RÃ, Dong H, Ribeiro J, Jiménez-Barbero J, Ramström O. Direct STDâ
NMR Identification of β-Galactosidase Inhibitors from a Virtual Dynamic Hemithioacetal System. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.200903920] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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Hiraoka S, Harano K, Nakamura T, Shiro M, Shionoya M. Induced-Fit Formation of a Tetrameric Organic Capsule Consisting of Hexagram-Shaped Amphiphile Molecules. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200902652] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Hiraoka S, Harano K, Nakamura T, Shiro M, Shionoya M. Induced-Fit Formation of a Tetrameric Organic Capsule Consisting of Hexagram-Shaped Amphiphile Molecules. Angew Chem Int Ed Engl 2009; 48:7006-9. [DOI: 10.1002/anie.200902652] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Xu XN, Wang L, Wang GT, Lin JB, Li GY, Jiang XK, Li ZT. Hydrogen-Bonding-Mediated Dynamic Covalent Synthesis of Macrocycles and Capsules: New Receptors for Aliphatic Ammonium Ions and the Formation of Pseudo[3]rotaxanes. Chemistry 2009; 15:5763-74. [DOI: 10.1002/chem.200900309] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Wagner N, Ashkenasy G. Systems chemistry: logic gates, arithmetic units, and network motifs in small networks. Chemistry 2009; 15:1765-75. [PMID: 19107891 DOI: 10.1002/chem.200801850] [Citation(s) in RCA: 94] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
A mixture of molecules can be regarded as a network if all the molecular components participate in some kind of interaction with other molecules--either physical or functional interactions. Template-assisted ligation reactions that direct replication processes can serve as the functional elements that connect two members of a chemical network. In such a process, the template does not necessarily catalyze its own formation, but rather the formation of another molecule, which in turn can operate as a template for reactions within the network medium. It was postulated that even networks made up of small numbers of molecules possess a wealth of molecular information sufficient to perform rather complex behavior. To probe this assumption, we have constructed virtual arrays consisting of three replicating molecules, in which dimer templates are capable of catalyzing reactants to form additional templates. By using realistic parameters from peptides or DNA replication experiments, we simulate the construction of various functional motifs within the networks. Specifically, we have designed and implemented each of the three-element Boolean logic gates, and show how these networks are assembled from four basic "building blocks". We also show how the catalytic pathways can be wired together to perform more complex arithmetic units and network motifs, such as the half adder and half subtractor computational modules, and the coherent feed-forward loop network motifs under different sets of parameters. As in previous studies of chemical networks, some of the systems described display behavior that would be difficult to predict without the numerical simulations. Furthermore, the simulations reveal trends and characteristics that should be useful as "recipes" for future design of experimental functional motifs and for potential integration into modular circuits and molecular computation devices.
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Affiliation(s)
- Nathaniel Wagner
- Department of Chemistry, Ben Gurion University of the Negev, Beer Sheva 84105, Israel
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Sadownik J, Philp D. A Simple Synthetic Replicator Amplifies Itself from a Dynamic Reagent Pool. Angew Chem Int Ed Engl 2008; 47:9965-70. [DOI: 10.1002/anie.200804223] [Citation(s) in RCA: 131] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Sadownik J, Philp D. A Simple Synthetic Replicator Amplifies Itself from a Dynamic Reagent Pool. Angew Chem Int Ed Engl 2008. [DOI: 10.1002/ange.200804223] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Nielsen MC, Ulven T. Selective Extraction of G-Quadruplex Ligands from a Rationally Designed Scaffold-Based Dynamic Combinatorial Library. Chemistry 2008; 14:9487-90. [DOI: 10.1002/chem.200801109] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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Corbett P, Sanders J, Otto S. Exploring the Relation between Amplification and Binding in Dynamic Combinatorial Libraries of Macrocyclic Synthetic Receptors in Water. Chemistry 2008; 14:2153-66. [DOI: 10.1002/chem.200701413] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Cacciapagliaa R, Di Stefanoa S, Mandolinia L. On the ‘livingness’ of a dynamic library of cyclophane formaldehyde acetals incorporating calix[4]arene subunits. J PHYS ORG CHEM 2008. [DOI: 10.1002/poc.1357] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Cacciapaglia R, Di Stefano S, Mandolini L, Mencarelli P, Ugozzoli F. Metathesis Reactions of Formaldehyde Acetals – Experimental and Computational Investigation of Isomeric Families of Cyclophanes under Dynamic Conditions. European J Org Chem 2008. [DOI: 10.1002/ejoc.200700906] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Vongvilai P, Angelin M, Larsson R, Ramström O. Dynamic combinatorial resolution: direct asymmetric lipase-mediated screening of a dynamic nitroaldol library. Angew Chem Int Ed Engl 2007; 46:948-50. [PMID: 17171748 DOI: 10.1002/anie.200603740] [Citation(s) in RCA: 89] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Pornrapee Vongvilai
- Department of Chemistry, KTH-Royal Institute of Technology, Teknikringen 30, 10044 Stockholm, Sweden
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Vongvilai P, Angelin M, Larsson R, Ramström O. Dynamic Combinatorial Resolution: Direct Asymmetric Lipase-Mediated Screening of a Dynamic Nitroaldol Library. Angew Chem Int Ed Engl 2007. [DOI: 10.1002/ange.200603740] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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Cacciapaglia R, Di Stefano S, Mandolini L. A Ring-Fusion/Ring-Fission Mechanism for the Metathesis Reaction of Macrocyclic Formaldehyde Acetals. Chemistry 2006; 12:8566-70. [PMID: 16983710 DOI: 10.1002/chem.200600983] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Important insight has been obtained into the mechanism of the reversible acid-catalysed transacetalation of cyclophane formaldehyde acetals (formals) C(i) in CDCl(3), at 25 degrees C. The order of appearance of the lowest oligomers in the early stages of the equilibration reaction is fully consistent with ring-fusion/ring-fission processes in which oxonium ion intermediates undergo S(N)2 reactions, according to an acid-catalysed bimolecular (A2) mechanism. The alternative acid-catalysed monomolecular (A1) reaction path, based on "back-biting" processes of carbenium ions generated by S(N)1-type cleavage of oxonium ion intermediates, predicts sequences that are in marked contrast with experimental findings.
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Affiliation(s)
- Roberta Cacciapaglia
- Dipartimento di Chimica e IMC-CNR Sezione Meccanismi di Reazione, Università di Roma La Sapienza, Box 34--Roma 62, 00185 Roma, Italy.
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