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Tobajas-Curiel G, Sun Q, Sanders JKM, Ballester P, Hunter CA. Substituent effects on aromatic interactions in water. Chem Sci 2023; 14:6226-6236. [PMID: 37325132 PMCID: PMC10266462 DOI: 10.1039/d3sc01027a] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 04/28/2023] [Indexed: 06/17/2023] Open
Abstract
Molecular recognition in water involves contributions due to polar functional group interactions, partial desolvation of polar and non-polar surfaces and changes in conformational flexibility, presenting a challenge for rational design and interpretation of supramolecular behaviour. Conformationally well-defined supramolecular complexes that can be studied in both water and non-polar solvents provide a platform for disentangling these contributions. Here 1 : 1 complexes formed between four different calix[4]pyrrole receptors and thirteen different pyridine N-oxide guests have been used to dissect the factors that govern substituent effects on aromatic interactions in water. H-bonding interactions between the receptor pyrrole donors and the guest N-oxide acceptor at one end of the complex lock the geometrical arrangement of a cluster of aromatic interactions at the other end of the complex, so that a phenyl group on the guest makes two edge-to-face and two stacking interactions with the four aromatic side-walls of the receptor. The thermodynamic contribution of these aromatic interactions to the overall stability of the complex was quantified by chemical double mutant cycles using isothermal titration calorimetry and 1H NMR competition experiments. Aromatic interactions between the receptor and a phenyl group on the guest stabilise the complex by a factor of 1000, and addition of substituents to the guest phenyl group further stabilises the complex by an additional factor of up to 1000. When a nitro substituent is present on the guest phenyl group, the complex has a sub-picomolar dissociation constant (370 fM). The remarkable substituent effects observed in water for these complexes can be rationalised by comparison with the magnitude of the corresponding substituent effects measured in chloroform. In chloroform, the double mutant cycle free energy measurements of the aromatic interactions correlate well with the substituent Hammett parameters. Electron-withdrawing substituents increase the strength of the interactions by a factor of up to 20, highlighting the role of electrostatics in stabilising both the edge-to-face and stacking interactions. The enhanced substituent effects observed in water are due to entropic contributions associated with the desolvation of hydrophobic surfaces on the substituents. The flexible alkyl chains that line the open end of the binding site assist the desolvation of the non-polar π-surfaces of polar substituents, like nitro, but at the same time allow water to interact with the polar H-bond acceptor sites on the substituent. This flexibility allows polar substituents to maximise non-polar interactions with the receptor and polar interactions with the solvent, leading to remarkably high binding affinities.
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Affiliation(s)
| | - Qingqing Sun
- Institute of Chemical Research of Catalonia (ICIQ), Barcelona Institute of Science and Technology (BIST) Av. Països Catalans, 16, 43007 Tarragona Spain
- Yangzhou University, School of Chemistry and Chemical Engineering Yangzhou 225002 Jiangsu China
| | - Jeremy K M Sanders
- Yusuf Hamied Department of Chemistry, University of Cambridge Cambridge CB2 1EW UK
| | - Pablo Ballester
- Institute of Chemical Research of Catalonia (ICIQ), Barcelona Institute of Science and Technology (BIST) Av. Països Catalans, 16, 43007 Tarragona Spain
- ICREA Passeig Lluís Companys 23 08010 Barcelona Spain
| | - Christopher A Hunter
- Yusuf Hamied Department of Chemistry, University of Cambridge Cambridge CB2 1EW UK
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Aliev AE, Motherwell WB. Some Recent Advances in the Design and Use of Molecular Balances for the Experimental Quantification of Intramolecular Noncovalent Interactions of π Systems. Chemistry 2019; 25:10516-10530. [DOI: 10.1002/chem.201900854] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2019] [Revised: 05/09/2019] [Indexed: 02/03/2023]
Affiliation(s)
- Abil E. Aliev
- Department of ChemistryUniversity College London 20 Gordon Street London WC1H 0AJ UK
| | - William B. Motherwell
- Department of ChemistryUniversity College London 20 Gordon Street London WC1H 0AJ UK
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3
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Kanao E, Kubo T, Naito T, Matsumoto T, Sano T, Yan M, Otsuka K. Differentiating π Interactions by Constructing Concave/Convex Surfaces Using a Bucky Bowl Molecule, Corannulene in Liquid Chromatography. Anal Chem 2018; 91:2439-2446. [DOI: 10.1021/acs.analchem.8b05260] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Eisuke Kanao
- Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Takuya Kubo
- Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Toyohiro Naito
- Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Takatoshi Matsumoto
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577, Japan
| | - Tomoharu Sano
- Center for Environmental Measurement and Analysis, National Institute for Environmental Studies, Onogawa 16-2, Tsukuba, Ibaraki 305-8506, Japan
| | - Mingdi Yan
- Department of Chemistry, University of Massachusetts Lowell, One University Avenue, Lowell, Massachusetts 01854, United States
| | - Koji Otsuka
- Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
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4
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González-Rosende ME, Castillo E, Jennings WB, Malone JF. Stereodynamics and edge-to-face CH-π aromatic interactions in imino compounds containing heterocyclic rings. Org Biomol Chem 2017; 15:1484-1494. [PMID: 28116383 DOI: 10.1039/c6ob02618d] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
By comparison with close contact interactions between benzene rings there is a paucity of experimental data available for attractive interactions involving aromatic heterocyclic rings, especially for small molecules in solution. Herein we describe aromatic heterocyclic and carbocyclic edge-to face interactions and conformational stereodynamics of N-1,2-diphenylethyl imines bearing a phenyl group and either a 2-pyridyl, 3-pyridyl, 2-thiophene or 2-furanyl moiety on the imino carbon. X-ray crystal structures have been determined for two compounds. Slow rotation about the phenyl-imino bond in the E-isomers and around the heterocycle-imino bond in the Z-isomers of the pyridyl compounds was observed at low temperatures by NMR. Abnormally large shielding of one ortho hydrogen indicates that both the imino phenyl and heterocycle rings can engage in an edge-to-face interaction with the N-terminal phenyl moiety in the appropriate isomer. Some rotational barriers around the phenyl-imino and heterocycle-imino bonds were measured.
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Affiliation(s)
- M Eugenia González-Rosende
- Departamento de Farmacia, Universidad CEU Cardenal Herrera, Avda. Seminario s/n, 46113, Moncada, Valencia, Spain.
| | - Encarna Castillo
- Departamento de Farmacia, Universidad CEU Cardenal Herrera, Avda. Seminario s/n, 46113, Moncada, Valencia, Spain.
| | - W Brian Jennings
- Department of Chemistry and Analytical & Biological Chemistry Research Facility, University College Cork, Cork, Ireland.
| | - John F Malone
- School of Chemistry & Chemical Engineering, The Queen's University of Belfast, Belfast BT9 5AG, UK
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5
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Yamada S, Yamamoto N, Takamori E. Synthesis of Molecular Seesaw Balances and the Evaluation of Pyridinium−π Interactions. J Org Chem 2016; 81:11819-11830. [DOI: 10.1021/acs.joc.6b02295] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Shinji Yamada
- Department of Chemistry, Faculty of Science, Ochanomizu University, 2-1-1 Otsuka, Bunkyo-ku,
Tokyo 112-8610, Japan
| | - Natsuo Yamamoto
- Department of Chemistry, Faculty of Science, Ochanomizu University, 2-1-1 Otsuka, Bunkyo-ku,
Tokyo 112-8610, Japan
| | - Eri Takamori
- Department of Chemistry, Faculty of Science, Ochanomizu University, 2-1-1 Otsuka, Bunkyo-ku,
Tokyo 112-8610, Japan
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6
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Gary DC, Flowers SE, Kaminsky W, Petrone A, Li X, Cossairt BM. Single-Crystal and Electronic Structure of a 1.3 nm Indium Phosphide Nanocluster. J Am Chem Soc 2016; 138:1510-3. [PMID: 26784649 DOI: 10.1021/jacs.5b13214] [Citation(s) in RCA: 88] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Magic-sized nanoclusters have been implicated as mechanistically relevant intermediates in the synthesis of group III-V quantum dots. Herein we report the single-crystal X-ray diffraction structure of a carboxylate-ligated indium phosphide magic-sized nanocluster at 0.83 Å resolution. The structure of this cluster, In37P20(O2CR)51, deviates from that of known crystal phases and possesses a non-stoichiometric, charged core composed of a series of fused 6-membered rings. The cluster is completely passivated by bidentate carboxylate ligands exhibiting predominantly bridging binding modes. The absorption spectrum of the cluster shows an asymmetric line shape that is broader than what would be expected from a homogeneous sample. A combination of computational and experimental evidence suggests that the spectral line width is a result of multiple, discrete electronic transitions that couple to vibrations of the nanocrystal lattice. The product of reaction of this nanocluster with 1 equiv of water has also been structurally characterized, demonstrating site selectivity without a drastic alteration of electronic structure.
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Affiliation(s)
- Dylan C Gary
- Department of Chemistry, University of Washington , Seattle, Washington 98195-1700, United States
| | - Sarah E Flowers
- Department of Chemistry, University of Washington , Seattle, Washington 98195-1700, United States
| | - Werner Kaminsky
- Department of Chemistry, University of Washington , Seattle, Washington 98195-1700, United States
| | - Alessio Petrone
- Department of Chemistry, University of Washington , Seattle, Washington 98195-1700, United States
| | - Xiaosong Li
- Department of Chemistry, University of Washington , Seattle, Washington 98195-1700, United States
| | - Brandi M Cossairt
- Department of Chemistry, University of Washington , Seattle, Washington 98195-1700, United States
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7
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Yamada S, Yamamoto N, Takamori E. A Molecular Seesaw Balance: Evaluation of Solvent and Counteranion Effects on Pyridinium−π Interactions. Org Lett 2015; 17:4862-5. [DOI: 10.1021/acs.orglett.5b02420] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Shinji Yamada
- Department of Chemistry,
Faculty of Science, Ochanomizu University, 2-1-1 Otsuka, Bunkyo-ku, Tokyo112-8610, Japan
| | - Natsuo Yamamoto
- Department of Chemistry,
Faculty of Science, Ochanomizu University, 2-1-1 Otsuka, Bunkyo-ku, Tokyo112-8610, Japan
| | - Eri Takamori
- Department of Chemistry,
Faculty of Science, Ochanomizu University, 2-1-1 Otsuka, Bunkyo-ku, Tokyo112-8610, Japan
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8
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Unusual reverse face-to-face stacking in propylene linked pyrazole system: perspective of organic materials. Struct Chem 2014. [DOI: 10.1007/s11224-014-0512-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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9
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Jennings WB, O'Connell N, Malone JF, Boyd DR. An evaluation of substituent effects on aromatic edge-to-face interactions and CF-π versus CH-π interactions using an imino torsion balance model. Org Biomol Chem 2014; 11:5278-91. [PMID: 23835675 DOI: 10.1039/c3ob40535d] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A selection of imines derived from phenyl t-butyl ketones and substituted 2-phenylethylamines or phenylalanine exhibit slow rotation around the aryl–imino bond at ambient temperature, resulting in a large non-equivalence of the ortho hydrogens in the 1H NMR spectra. This facilitates assessment of aryl substituent effects on the face tilted-T CH–π interaction between a phenyl ring (A) on the imino carbon proximate to the terminal phenyl ring (B). Analysis of the marked temperature dependence of the chemical shift of the interacting ortho hydrogen affords estimates of the opposing enthalpic and entropic factors involved in the rapid equilibrium between the closed edge-to-face conformation and alternative open conformations devoid of a CH–π interaction while in solution. Above ca. 80 °C the entropy term (TΔS) cancels out the enthalpy (ΔH) favouring the closed conformation and open conformations are preferred. Accordingly, commonly reported binding free energies may not be a good measure of the energetic strength of intramolecular aromatic interactions. Investigation of an ortho fluoro substituted compound indicates that a CF–π interaction is at least 1.0 kcal mol−1 weaker in enthalpy than the CH–π interaction. Several X-ray crystal structures depicting an intramolecular edge-to-face interaction are presented.
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Affiliation(s)
- W Brian Jennings
- Department of Chemistry and Analytical & Biological Chemistry Research Facility, University College Cork, Cork, Ireland.
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10
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Choudhary U, Northrop BH. Allyl-Functionalized Dioxynaphthalene[38]Crown-10 Macrocycles: Synthesis, Self-Assembly, and Thiol-ene Functionalization. Chemistry 2013; 20:999-1009. [DOI: 10.1002/chem.201303864] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2013] [Indexed: 12/26/2022]
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11
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Barman AK, Verma S. Solid state structures and solution phase self-assembly of clicked mannosylated diketopiperazines. RSC Adv 2013. [DOI: 10.1039/c3ra42310g] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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12
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Cardellicchio C, Capozzi MAM, Alvarez-Larena A, Piniella JF, Capitelli F. Investigation on the weak interactions assembling the crystal structures of Betti bases. CrystEngComm 2012. [DOI: 10.1039/c2ce06295j] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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13
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Mazzanti A, Casarini D. Recent trends in conformational analysis. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2011. [DOI: 10.1002/wcms.96] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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14
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Takahashi O, Kohno Y, Nishio M. Relevance of weak hydrogen bonds in the conformation of organic compounds and bioconjugates: evidence from recent experimental data and high-level ab initio MO calculations. Chem Rev 2011; 110:6049-76. [PMID: 20550180 DOI: 10.1021/cr100072x] [Citation(s) in RCA: 447] [Impact Index Per Article: 34.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Osamu Takahashi
- Department of Chemistry, Graduate School of Science, Hiroshima University, Kagamiyama, Higashi-Hiroshima, 739-8526, Japan.
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15
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Nilsson Lill SO. Evaluation of dispersion-corrected density functional theory (B3LYP-DCP) for compounds of biochemical interest. J Mol Graph Model 2010; 29:178-87. [DOI: 10.1016/j.jmgm.2010.06.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2010] [Revised: 06/01/2010] [Accepted: 06/02/2010] [Indexed: 11/16/2022]
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