1
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Lidskog A, Dawaigher S, Solano Arribas C, Ryberg A, Jensen J, Bergquist KE, Sundin A, Norrby PO, Wärnmark K. Experimental and Computational Models for Side Chain Discrimination in Peptide-Protein Interactions. Chemistry 2021; 27:10883-10897. [PMID: 33908678 PMCID: PMC8362025 DOI: 10.1002/chem.202100890] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Indexed: 12/02/2022]
Abstract
A bis(18‐crown‐6) Tröger's base receptor and 4‐substituted hepta‐1,7‐diyl bisammonium salt ligands have been used as a model system to study the interactions between non‐polar side chains of peptides and an aromatic cavity of a protein. NMR titrations and NOESY/ROESY NMR spectroscopy were used to analyze the discrimination of the ligands by the receptor based on the substituent of the ligand, both quantitatively (free binding energies) and qualitatively (conformations). The analysis showed that an all‐anti conformation of the heptane chain was preferred for most of the ligands, both free and when bound to the receptor, and that for all of the receptor‐ligand complexes, the substituent was located inside or partly inside of the aromatic cavity of the receptor. We estimated the free binding energy of a methyl‐ and a phenyl group to an aromatic cavity, via CH‐π, and combined aromatic CH‐π and π‐π interactions to be −1.7 and −3.3 kJ mol−1, respectively. The experimental results were used to assess the accuracy of different computational methods, including molecular mechanics (MM) and density functional theory (DFT) methods, showing that MM was superior.
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Affiliation(s)
- Anna Lidskog
- Centre for Analysis and Synthesis, Department of Chemistry, Lund University, P. O Box 124, S-221 00, Lund, Sweden
| | - Sami Dawaigher
- Centre for Analysis and Synthesis, Department of Chemistry, Lund University, P. O Box 124, S-221 00, Lund, Sweden
| | - Carlos Solano Arribas
- Centre for Analysis and Synthesis, Department of Chemistry, Lund University, P. O Box 124, S-221 00, Lund, Sweden
| | - Anna Ryberg
- Centre for Analysis and Synthesis, Department of Chemistry, Lund University, P. O Box 124, S-221 00, Lund, Sweden
| | - Jacob Jensen
- Centre for Analysis and Synthesis, Department of Chemistry, Lund University, P. O Box 124, S-221 00, Lund, Sweden
| | - Karl Erik Bergquist
- Centre for Analysis and Synthesis, Department of Chemistry, Lund University, P. O Box 124, S-221 00, Lund, Sweden
| | - Anders Sundin
- Centre for Analysis and Synthesis, Department of Chemistry, Lund University, P. O Box 124, S-221 00, Lund, Sweden
| | - Per-Ola Norrby
- Data Science & Modelling, Pharmaceutical Sciences, R&D, AstraZeneca Gothenburg, Gothenburg, Sweden
| | - Kenneth Wärnmark
- Centre for Analysis and Synthesis, Department of Chemistry, Lund University, P. O Box 124, S-221 00, Lund, Sweden
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2
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Yamada M, Narita H, Maeda Y. A Fullerene‐Based Molecular Torsion Balance for Investigating Noncovalent Interactions at the C
60
Surface. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202005888] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Michio Yamada
- Department of Chemistry Tokyo Gakugei University Nukuikitamachi 4-1-1 Koganei Tokyo 184-8501 Japan
| | - Haruna Narita
- Department of Chemistry Tokyo Gakugei University Nukuikitamachi 4-1-1 Koganei Tokyo 184-8501 Japan
| | - Yutaka Maeda
- Department of Chemistry Tokyo Gakugei University Nukuikitamachi 4-1-1 Koganei Tokyo 184-8501 Japan
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Yamada M, Narita H, Maeda Y. A Fullerene-Based Molecular Torsion Balance for Investigating Noncovalent Interactions at the C 60 Surface. Angew Chem Int Ed Engl 2020; 59:16133-16140. [PMID: 32458522 DOI: 10.1002/anie.202005888] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Indexed: 12/12/2022]
Abstract
To investigate the nature and strength of noncovalent interactions at the fullerene surface, molecular torsion balances consisting of C60 and organic moieties connected through a biphenyl linkage were synthesized. NMR and computational studies show that the unimolecular system remains in equilibrium between well-defined folded and unfolded conformers owing to restricted rotation around the biphenyl C-C bond. The energy differences between the two conformers depend on the substituents and is ascribed to differences in the intramolecular noncovalent interactions between the organic moieties and the fullerene surface. Fullerenes favor interacting with the π-faces of benzenes bearing electron-donating substituents. The correlation between the folding free energies and corresponding Hammett constants of the substituents in the arene-containing torsion balances reflects the contributions of the electrostatic interactions and dispersion force to face-to-face arene-fullerene interactions.
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Affiliation(s)
- Michio Yamada
- Department of Chemistry, Tokyo Gakugei University, Nukuikitamachi 4-1-1, Koganei, Tokyo, 184-8501, Japan
| | - Haruna Narita
- Department of Chemistry, Tokyo Gakugei University, Nukuikitamachi 4-1-1, Koganei, Tokyo, 184-8501, Japan
| | - Yutaka Maeda
- Department of Chemistry, Tokyo Gakugei University, Nukuikitamachi 4-1-1, Koganei, Tokyo, 184-8501, Japan
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Ling X, Wilcox CS. A Molecular Torsion Balance Study: A Nearby Anionic Group Exerts Little Influence on Hydrophobic Interactions between Nonpolar Surfaces. Chemistry 2019; 25:14010-14014. [PMID: 30913319 PMCID: PMC6763384 DOI: 10.1002/chem.201901208] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Indexed: 11/10/2022]
Abstract
Polar groups have a solvent ordering effect on water and therefore may affect hydrophobic binding energies for nearby lipophilic surfaces. This would mean that determinations of excess surface free energy association energies require consideration of nearby polar functional groups. This paper reports results of a study to measure this possible effect. It was concluded from the models used here that an anionic polar group nearby a hydrophobic surface has little or no effect on the magnitude of hydrophobic association.
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Affiliation(s)
- Xiujun Ling
- HM Health Solutions Inc., Pittsburgh, PA, 15222, USA
| | - Craig S Wilcox
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, 15260, USA
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5
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Lungerich D, Hitzenberger JF, Hampel F, Drewello T, Jux N. Superbenzene-Porphyrin Gas-Phase Architectures Derived from Intermolecular Dispersion Interactions. Chemistry 2018; 24:15818-15824. [DOI: 10.1002/chem.201803684] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Indexed: 12/12/2022]
Affiliation(s)
- Dominik Lungerich
- Department of Chemistry and Pharmacy & Interdisciplinary, Center for Molecular Materials (ICMM), Organic Chemistry II; Friedrich-Alexander-University Erlangen-Nuernberg; Nikolaus-Fiebiger-Str. 10 90458 Erlangen Germany
- Department of Chemistry & Molecular Technology Innovation Chair; University of Tokyo; 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
| | - Jakob F. Hitzenberger
- Department of Chemistry and Pharmacy; Physical Chemistry I; Friedrich-Alexander-University Erlangen-Nuernberg; Egerlandstr. 3 90458 Erlangen Germany
| | - Frank Hampel
- Department of Chemistry and Pharmacy & Interdisciplinary, Center for Molecular Materials (ICMM), Organic Chemistry II; Friedrich-Alexander-University Erlangen-Nuernberg; Nikolaus-Fiebiger-Str. 10 90458 Erlangen Germany
| | - Thomas Drewello
- Department of Chemistry and Pharmacy; Physical Chemistry I; Friedrich-Alexander-University Erlangen-Nuernberg; Egerlandstr. 3 90458 Erlangen Germany
| | - Norbert Jux
- Department of Chemistry and Pharmacy & Interdisciplinary, Center for Molecular Materials (ICMM), Organic Chemistry II; Friedrich-Alexander-University Erlangen-Nuernberg; Nikolaus-Fiebiger-Str. 10 90458 Erlangen Germany
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6
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Motherwell WB, Moreno RB, Pavlakos I, Arendorf JRT, Arif T, Tizzard GJ, Coles SJ, Aliev AE. Noncovalent Interactions of π Systems with Sulfur: The Atomic Chameleon of Molecular Recognition. Angew Chem Int Ed Engl 2017; 57:1193-1198. [DOI: 10.1002/anie.201708485] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Revised: 11/16/2017] [Indexed: 12/24/2022]
Affiliation(s)
- William B. Motherwell
- Department of Chemistry; University College London; 20 Gordon Street London WC1H 0AJ UK
| | - Rafael B. Moreno
- Department of Chemistry; University College London; 20 Gordon Street London WC1H 0AJ UK
| | - Ilias Pavlakos
- Department of Chemistry; University College London; 20 Gordon Street London WC1H 0AJ UK
| | | | - Tanzeel Arif
- Department of Chemistry; University College London; 20 Gordon Street London WC1H 0AJ UK
| | - Graham J. Tizzard
- School of Chemistry; University of Southampton; University Road Southampton SO17 1BJ UK
| | - Simon J. Coles
- School of Chemistry; University of Southampton; University Road Southampton SO17 1BJ UK
| | - Abil E. Aliev
- Department of Chemistry; University College London; 20 Gordon Street London WC1H 0AJ UK
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7
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Motherwell WB, Moreno RB, Pavlakos I, Arendorf JRT, Arif T, Tizzard GJ, Coles SJ, Aliev AE. Noncovalent Interactions of π Systems with Sulfur: The Atomic Chameleon of Molecular Recognition. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201708485] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- William B. Motherwell
- Department of Chemistry; University College London; 20 Gordon Street London WC1H 0AJ UK
| | - Rafael B. Moreno
- Department of Chemistry; University College London; 20 Gordon Street London WC1H 0AJ UK
| | - Ilias Pavlakos
- Department of Chemistry; University College London; 20 Gordon Street London WC1H 0AJ UK
| | | | - Tanzeel Arif
- Department of Chemistry; University College London; 20 Gordon Street London WC1H 0AJ UK
| | - Graham J. Tizzard
- School of Chemistry; University of Southampton; University Road Southampton SO17 1BJ UK
| | - Simon J. Coles
- School of Chemistry; University of Southampton; University Road Southampton SO17 1BJ UK
| | - Abil E. Aliev
- Department of Chemistry; University College London; 20 Gordon Street London WC1H 0AJ UK
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8
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Pavlakos I, Arif T, Aliev AE, Motherwell WB, Tizzard GJ, Coles SJ. Noncovalent Lone Pair⋅⋅⋅(No-π!)-Heteroarene Interactions: The Janus-Faced Hydroxy Group. Angew Chem Int Ed Engl 2015; 54:8169-74. [DOI: 10.1002/anie.201502103] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Indexed: 11/10/2022]
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9
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Pavlakos I, Arif T, Aliev AE, Motherwell WB, Tizzard GJ, Coles SJ. Noncovalent Lone Pair⋅⋅⋅(No-π!)-Heteroarene Interactions: The Janus-Faced Hydroxy Group. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201502103] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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10
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Harder M, Carnero Corrales MA, Trapp N, Kuhn B, Diederich F. Rebek Imide Platforms as Model Systems for the Investigation of Weak Intermolecular Interactions. Chemistry 2015; 21:8455-63. [DOI: 10.1002/chem.201500462] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Indexed: 11/09/2022]
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11
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Persch E, Dumele O, Diederich F. Molekulare Erkennung in chemischen und biologischen Systemen. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201408487] [Citation(s) in RCA: 102] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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12
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Persch E, Dumele O, Diederich F. Molecular recognition in chemical and biological systems. Angew Chem Int Ed Engl 2015; 54:3290-327. [PMID: 25630692 DOI: 10.1002/anie.201408487] [Citation(s) in RCA: 419] [Impact Index Per Article: 46.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Indexed: 12/13/2022]
Abstract
Structure-based ligand design in medicinal chemistry and crop protection relies on the identification and quantification of weak noncovalent interactions and understanding the role of water. Small-molecule and protein structural database searches are important tools to retrieve existing knowledge. Thermodynamic profiling, combined with X-ray structural and computational studies, is the key to elucidate the energetics of the replacement of water by ligands. Biological receptor sites vary greatly in shape, conformational dynamics, and polarity, and require different ligand-design strategies, as shown for various case studies. Interactions between dipoles have become a central theme of molecular recognition. Orthogonal interactions, halogen bonding, and amide⋅⋅⋅π stacking provide new tools for innovative lead optimization. The combination of synthetic models and biological complexation studies is required to gather reliable information on weak noncovalent interactions and the role of water.
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Affiliation(s)
- Elke Persch
- Laboratorium für Organische Chemie, Departement Chemie und Angewandte Biowissenschaften, ETH Zürich, Vladimir-Prelog-Weg 3, 8093 Zürich (Switzerland)
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13
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Adam C, Yang L, Cockroft SL. Partitioning Solvophobic and Dispersion Forces in Alkyl and Perfluoroalkyl Cohesion. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201408982] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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14
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Adam C, Yang L, Cockroft SL. Partitioning Solvophobic and Dispersion Forces in Alkyl and Perfluoroalkyl Cohesion. Angew Chem Int Ed Engl 2014; 54:1164-7. [DOI: 10.1002/anie.201408982] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Indexed: 11/07/2022]
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15
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Aliev AE, Arendorf JRT, Pavlakos I, Moreno RB, Porter MJ, Rzepa HS, Motherwell WB. Surfing π Clouds for Noncovalent Interactions: Arenes versus Alkenes. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201409672] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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16
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Aliev AE, Arendorf JRT, Pavlakos I, Moreno RB, Porter MJ, Rzepa HS, Motherwell WB. Surfing π Clouds for Noncovalent Interactions: Arenes versus Alkenes. Angew Chem Int Ed Engl 2014; 54:551-5. [DOI: 10.1002/anie.201409672] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Indexed: 11/07/2022]
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17
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Whiting AL, Dubicki KI, Hof F. Synthesis of Versatile Nonsymmetric Amine- and Boron-Functionalized Tröger's Base Derivatives, Including a Tröger's Base Amino Acid. European J Org Chem 2013. [DOI: 10.1002/ejoc.201300992] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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18
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Rúnarsson ÖV, Artacho J, Wärnmark K. The 125thAnniversary of the Tröger's Base Molecule: Synthesis and Applications of Tröger's Base Analogues. European J Org Chem 2012. [DOI: 10.1002/ejoc.201201249] [Citation(s) in RCA: 113] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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19
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Benkhäuser-Schunk C, Wezisla B, Urbahn K, Kiehne U, Daniels J, Schnakenburg G, Neese F, Lützen A. Synthesis, Chiral Resolution, and Absolute Configuration of Functionalized Tröger’s Base Derivatives: Part II. Chempluschem 2012. [DOI: 10.1002/cplu.201200029] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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20
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Artacho J, Ascic E, Rantanen T, Karlsson J, Wallentin CJ, Wang R, Wendt OF, Harmata M, Snieckus V, Wärnmark K. Twisted Amide Analogues of Tröger’s Base. Chemistry 2012; 18:1038-42. [DOI: 10.1002/chem.201103228] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2011] [Indexed: 11/07/2022]
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Salonen LM, Ellermann M, Diederich F. Aromatische Ringe in chemischer und biologischer Erkennung: Energien und Strukturen. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201007560] [Citation(s) in RCA: 245] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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22
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Salonen LM, Ellermann M, Diederich F. Aromatic rings in chemical and biological recognition: energetics and structures. Angew Chem Int Ed Engl 2011; 50:4808-42. [PMID: 21538733 DOI: 10.1002/anie.201007560] [Citation(s) in RCA: 1167] [Impact Index Per Article: 89.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2010] [Indexed: 12/12/2022]
Abstract
This review describes a multidimensional treatment of molecular recognition phenomena involving aromatic rings in chemical and biological systems. It summarizes new results reported since the appearance of an earlier review in 2003 in host-guest chemistry, biological affinity assays and biostructural analysis, data base mining in the Cambridge Structural Database (CSD) and the Protein Data Bank (PDB), and advanced computational studies. Topics addressed are arene-arene, perfluoroarene-arene, S⋅⋅⋅aromatic, cation-π, and anion-π interactions, as well as hydrogen bonding to π systems. The generated knowledge benefits, in particular, structure-based hit-to-lead development and lead optimization both in the pharmaceutical and in the crop protection industry. It equally facilitates the development of new advanced materials and supramolecular systems, and should inspire further utilization of interactions with aromatic rings to control the stereochemical outcome of synthetic transformations.
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Affiliation(s)
- Laura M Salonen
- Laboratory of Organic Chemistry, Department of Chemistry and Applied Biosciences, ETH Zurich, Hönggerberg, HCI, 8093 Zurich, Switzerland
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23
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Giordano L, Hoang CT, Shipman M, Tucker JHR, Walsh TR. Aziridine Scaffolds for the Detection and Quantification of Hydrogen-Bonding Interactions through Transition-State Stabilization. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201005580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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24
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Giordano L, Hoang CT, Shipman M, Tucker JHR, Walsh TR. Aziridine scaffolds for the detection and quantification of hydrogen-bonding interactions through transition-state stabilization. Angew Chem Int Ed Engl 2011; 50:741-4. [PMID: 21226167 DOI: 10.1002/anie.201005580] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2010] [Revised: 10/26/2010] [Indexed: 11/05/2022]
Affiliation(s)
- Luciana Giordano
- School of Chemistry, University of Birmingham, Edgbaston, Birmingham, B15 2TT UK
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Carrillo R, López-Rodríguez M, Martín V, Martín T. Quantification of a CH-π Interaction Responsible for Chiral Discrimination and Evaluation of Its Contribution to Enantioselectivity. Angew Chem Int Ed Engl 2009; 48:7803-8. [DOI: 10.1002/anie.200903281] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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26
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Carrillo R, López-Rodríguez M, Martín V, Martín T. Quantification of a CH-π Interaction Responsible for Chiral Discrimination and Evaluation of Its Contribution to Enantioselectivity. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200903281] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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27
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Nguyen T, Sinclair D, Willis A, Sherburn M. Guest Binding Drives Reversible Atropisomerism in Cavitand Hosts. Chemistry 2009; 15:5892-5. [DOI: 10.1002/chem.200900695] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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28
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Kiehne U, Weilandt T, Lützen A. Self-Assembly of Dinuclear Double- and Triple-Stranded Helicates from Bis(bipyridine) Ligands Derived from Tröger's Base Analogues. European J Org Chem 2008. [DOI: 10.1002/ejoc.200701215] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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