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Stereodynamics of E/ Z isomerization in rotaxanes through mechanical shuttling and covalent bond rotation. Chem 2021; 7:2137-2150. [PMID: 34435161 PMCID: PMC8367298 DOI: 10.1016/j.chempr.2021.04.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 01/18/2021] [Accepted: 04/19/2021] [Indexed: 11/20/2022]
Abstract
The mechanical bond has opened a new world for structural and dynamic stereochemistry, which is still largely underexplored and whose significance for various applications is becoming increasingly evident. We demonstrate that designed rearrangements involving both covalent and mechanical bonds can be integrated in [2]rotaxanes, leading to interesting consequences in terms of E/Z isomerization mechanisms. Two entirely distinct and concomitant stereomutations, pertaining to the same stereogenic element but involving different kinds of linkages within the molecule, are observed and are thoroughly characterized. The rate of the two processes is affected in opposite ways upon changing solvent polarity; such a phenomenon can be used to selectively modify the rate of each motion and adjust the relative contribution of the two mechanisms to the isomerization. Although the movements are not synchronized, an analysis of the intriguing fundamental implications for transition state theory, reaction pathway bifurcation, and microscopic reversibility was triggered by our experimental observations. Rotaxanes that display E/Z stereoisomerism depending on the ring position Co-existence of two different stereomutations that yield the same product Mutual influence and opposite solvent dependence of the two dynamic processes Fundamental implications for microscopic reversibility and chemical equilibrium
The concurrence and interplay of different movements of molecular components within the same structure play a key role in providing function to naturally occurring molecular machines. Despite the progress made on artificial counterparts, the construction of molecular systems, where two (or more) motions are integrated together to produce an outcome, is still in its infancy. Molecules called rotaxanes, obtained by interlocking a ring with a dumbbell-shaped axle, are an appealing yet underexplored platform for this purpose. Here, we describe rotaxanes where two coexisting and radically different processes—rotation about a covalent bond and translation of the ring along the axle—lead to the same change in the overall molecular shape. These results are significant not only to improve our fundamental understanding of the way molecular components move but also to develop sophisticated artificial nanomachines capable of transforming or transmitting motion.
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P. Copetti JP, Salbego PRS, Orlando T, Rosa JML, Fiss GF, G. de Oliveira JP, A. Vasconcellos MLA, Zanatta N, G. Bonacorso H, Martins MAP. Substituent effects on the crystallization mechanisms of 7-chloro-4-substituted-quinolines. CrystEngComm 2020. [DOI: 10.1039/d0ce00214c] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The crystallization mechanisms of a series of fourteen 7-chloro-4-substituted-quinolines were proposed based on a retrocrystallization approach using the supramolecular cluster as demarcation.
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Affiliation(s)
- João P. P. Copetti
- Núcleo de Química de Heterociclos (NUQUIMHE)
- Department of Chemistry
- Federal University of Santa Maria (UFSM)
- Santa Maria
- Brazil
| | - Paulo R. S. Salbego
- Núcleo de Química de Heterociclos (NUQUIMHE)
- Department of Chemistry
- Federal University of Santa Maria (UFSM)
- Santa Maria
- Brazil
| | - Tainára Orlando
- Núcleo de Química de Heterociclos (NUQUIMHE)
- Department of Chemistry
- Federal University of Santa Maria (UFSM)
- Santa Maria
- Brazil
| | - Jéssica M. L. Rosa
- Núcleo de Química de Heterociclos (NUQUIMHE)
- Department of Chemistry
- Federal University of Santa Maria (UFSM)
- Santa Maria
- Brazil
| | - Gabriela F. Fiss
- Department of Chemistry
- Federal University of Paraíba (UFPB)
- João Pessoa
- Brazil
| | | | | | - Nilo Zanatta
- Núcleo de Química de Heterociclos (NUQUIMHE)
- Department of Chemistry
- Federal University of Santa Maria (UFSM)
- Santa Maria
- Brazil
| | - Helio G. Bonacorso
- Núcleo de Química de Heterociclos (NUQUIMHE)
- Department of Chemistry
- Federal University of Santa Maria (UFSM)
- Santa Maria
- Brazil
| | - Marcos A. P. Martins
- Núcleo de Química de Heterociclos (NUQUIMHE)
- Department of Chemistry
- Federal University of Santa Maria (UFSM)
- Santa Maria
- Brazil
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Salbego PRS, Bender CR, Orlando T, Moraes GA, Copetti JPP, Weimer GH, Bonacorso HG, Zanatta N, Hoerner M, Martins MAP. Supramolecular Similarity in Polymorphs: Use of Similarity Indices (I X). ACS OMEGA 2019; 4:9697-9709. [PMID: 31460060 PMCID: PMC6648757 DOI: 10.1021/acsomega.8b03660] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Accepted: 05/08/2019] [Indexed: 05/11/2023]
Abstract
A systematic investigation to assess the degree of similarity between polymorphs was carried out. A similarity indices (IX) approach was applied in ten series of polymorphs with different characteristics and number of molecules in the asymmetric unit. Geometric (ID), contact area (IC), and stabilization energy (IG) parameters were used. It was possible to situate each comparison in different regions of similarity within the polymorphism phenomenon and determine the boundaries between quasi-isostructural polymorphs and polymorphs of low similarity. The multiparameter IDCG index was used as a robust tool to determine the total similarity within the polymorphism phenomenon. The highest contribution of the stabilization energy parameter (45%) toward the final value of similarity (IDCG) was observed, followed by the contact area index (32%). The geometric index contributed approximately 23% to the final value of IDCG. This information reinforces the importance of the contact area and stabilization energy in assessing the degree of similarity between crystalline structures. A new descriptor (IQ) based on the comparison of the energetic contribution of intermolecular interaction types present in each crystal structure is presented. IQ can be a versatile tool and applicable even for systems that do not share any similarity.
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Affiliation(s)
- Paulo R. S. Salbego
- Núcleo de Química
de Heterociclos (NUQUIMHE) and Núcleo
de Investigação de Triazenos e Complexos (NITRICO),
Department of Chemistry, Federal University
of Santa Maria (UFSM), 97105-900 Santa Maria, RS, Brazil
- E-mail: (P.R.S.S.)
| | - Caroline R. Bender
- Núcleo de Química
de Heterociclos (NUQUIMHE) and Núcleo
de Investigação de Triazenos e Complexos (NITRICO),
Department of Chemistry, Federal University
of Santa Maria (UFSM), 97105-900 Santa Maria, RS, Brazil
| | - Tainára Orlando
- Núcleo de Química
de Heterociclos (NUQUIMHE) and Núcleo
de Investigação de Triazenos e Complexos (NITRICO),
Department of Chemistry, Federal University
of Santa Maria (UFSM), 97105-900 Santa Maria, RS, Brazil
| | - Guilherme A. Moraes
- Núcleo de Química
de Heterociclos (NUQUIMHE) and Núcleo
de Investigação de Triazenos e Complexos (NITRICO),
Department of Chemistry, Federal University
of Santa Maria (UFSM), 97105-900 Santa Maria, RS, Brazil
| | - João P. P. Copetti
- Núcleo de Química
de Heterociclos (NUQUIMHE) and Núcleo
de Investigação de Triazenos e Complexos (NITRICO),
Department of Chemistry, Federal University
of Santa Maria (UFSM), 97105-900 Santa Maria, RS, Brazil
| | - Gustavo H. Weimer
- Núcleo de Química
de Heterociclos (NUQUIMHE) and Núcleo
de Investigação de Triazenos e Complexos (NITRICO),
Department of Chemistry, Federal University
of Santa Maria (UFSM), 97105-900 Santa Maria, RS, Brazil
| | - Helio G. Bonacorso
- Núcleo de Química
de Heterociclos (NUQUIMHE) and Núcleo
de Investigação de Triazenos e Complexos (NITRICO),
Department of Chemistry, Federal University
of Santa Maria (UFSM), 97105-900 Santa Maria, RS, Brazil
| | - Nilo Zanatta
- Núcleo de Química
de Heterociclos (NUQUIMHE) and Núcleo
de Investigação de Triazenos e Complexos (NITRICO),
Department of Chemistry, Federal University
of Santa Maria (UFSM), 97105-900 Santa Maria, RS, Brazil
| | - Manfredo Hoerner
- Núcleo de Química
de Heterociclos (NUQUIMHE) and Núcleo
de Investigação de Triazenos e Complexos (NITRICO),
Department of Chemistry, Federal University
of Santa Maria (UFSM), 97105-900 Santa Maria, RS, Brazil
| | - Marcos A. P. Martins
- Núcleo de Química
de Heterociclos (NUQUIMHE) and Núcleo
de Investigação de Triazenos e Complexos (NITRICO),
Department of Chemistry, Federal University
of Santa Maria (UFSM), 97105-900 Santa Maria, RS, Brazil
- E-mail: (M.A.P.M)
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McGarraugh HH, Liu W, Matthews BP, Smith BD. Croconaine Rotaxane Dye with 984 nm Absorption: Wavelength-Selective Photothermal Heating. European J Org Chem 2019; 2019:3489-3494. [PMID: 31579392 PMCID: PMC6774672 DOI: 10.1002/ejoc.201900082] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Indexed: 01/02/2023]
Abstract
Croconaines are an emerging class of near-infrared dyes that are useful for various sensing, photothermal, optoelectronic, and photoacoustic applications. Previous work encapsulated a dumbbell-shaped croconaine dye whose structure contains two thiophene flanking units inside a tetralactam macrocycle and produced a croconaine rotaxane 1 with a narrow 824 nm absorption band. Herein, a new rotaxane 2 is reported that encapsulates a croconaine dye with two thienothiophene flanking units. The new croconaine rotaxane 2 exhibits a narrow 984 nm absorption band that is distinct from the 824 nm absorption of rotaxane 1. Photothermal heating experiments showed that an 830 nm diode laser selectively heats a solution containing rotaxane 1, with no heating of a solution containing rotaxane 2. Conversely, a 980 nm diode laser selectively heats a solution containing rotaxane 2, with no heating of a solution containing rotaxane 1. The new croconaine rotaxane 2 shows no fatigue after four cycles of laser heating and cooling.
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Affiliation(s)
- Hannah H. McGarraugh
- Department of Chemistry and Biochemistry236 Nieuwland Science Hall, University of Notre Dame, IN 46556, USA
| | - Wenqi Liu
- Department of Chemistry and Biochemistry236 Nieuwland Science Hall, University of Notre Dame, IN 46556, USA
| | - Braden P. Matthews
- Department of Chemistry and Biochemistry236 Nieuwland Science Hall, University of Notre Dame, IN 46556, USA
| | - Bradley D. Smith
- Department of Chemistry and Biochemistry236 Nieuwland Science Hall, University of Notre Dame, IN 46556, USA
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Orlando T, Salbego PRS, Farias FFS, Weimer GH, Copetti JPP, Bonacorso HG, Zanatta N, Hoerner M, Berná J, Martins MAP. Crystallization Mechanisms Applied to Understand the Crystal Formation of Rotaxanes. European J Org Chem 2019. [DOI: 10.1002/ejoc.201801870] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Tainára Orlando
- Núcleo de Química de Heterociclos (NUQUIMHE); Department of Chemistry; Federal University of Santa Maria (UFSM); 97105-900 Santa Maria RS Brazil
| | - Paulo R. S. Salbego
- Núcleo de Química de Heterociclos (NUQUIMHE); Department of Chemistry; Federal University of Santa Maria (UFSM); 97105-900 Santa Maria RS Brazil
| | - Fellipe F. S. Farias
- Núcleo de Química de Heterociclos (NUQUIMHE); Department of Chemistry; Federal University of Santa Maria (UFSM); 97105-900 Santa Maria RS Brazil
| | - Gustavo H. Weimer
- Núcleo de Química de Heterociclos (NUQUIMHE); Department of Chemistry; Federal University of Santa Maria (UFSM); 97105-900 Santa Maria RS Brazil
| | - João P. P. Copetti
- Núcleo de Química de Heterociclos (NUQUIMHE); Department of Chemistry; Federal University of Santa Maria (UFSM); 97105-900 Santa Maria RS Brazil
| | - Helio G. Bonacorso
- Núcleo de Química de Heterociclos (NUQUIMHE); Department of Chemistry; Federal University of Santa Maria (UFSM); 97105-900 Santa Maria RS Brazil
| | - Nilo Zanatta
- Núcleo de Química de Heterociclos (NUQUIMHE); Department of Chemistry; Federal University of Santa Maria (UFSM); 97105-900 Santa Maria RS Brazil
| | - Manfredo Hoerner
- Núcleo de Investigação de Triazenos e Complexos (NITRICO); Departmento de Química; Federal University of Santa Maria (UFSM); 97105-900 Santa Maria RS Brazil
| | - José Berná
- Departmento de Química Orgánica; Faculdad de Química; Universidad de Murcia; 30100 Murcia Spain
| | - Marcos A. P. Martins
- Núcleo de Química de Heterociclos (NUQUIMHE); Department of Chemistry; Federal University of Santa Maria (UFSM); 97105-900 Santa Maria RS Brazil
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Li DH, Smith BD. Molecular recognition using tetralactam macrocycles with parallel aromatic sidewalls. Beilstein J Org Chem 2019; 15:1086-1095. [PMID: 31164945 PMCID: PMC6541352 DOI: 10.3762/bjoc.15.105] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 05/02/2019] [Indexed: 01/16/2023] Open
Abstract
This review summarizes the supramolecular properties of tetralactam macrocycles that have parallel aromatic sidewalls and four NH residues directed into the macrocyclic cavity. These macrocycles are versatile hosts for a large number of different guest structures in water and organic solvents, and they are well-suited for a range of supramolecular applications. The macrocyclic cavity contains a mixture of polar functional groups and non-polar surfaces which is reminiscent of the amphiphilic binding pockets within many proteins. In water, the aromatic surfaces in the tetralactam cavity drive high affinity due the hydrophobic effect and the NH groups provide secondary interactions that induce binding selectivity. In organic solvents, the supramolecular factors are reversed; the polar NH groups drive high affinity and the aromatic surfaces provide the secondary interactions. In addition to an amphiphilic cavity, macrocyclic tetralactams exhibit conformational flexibility, and the combination of properties enables them to be effective hosts for a wide range of guest molecules including organic biscarbonyl derivatives, near-infrared dyes, acenes, precious metal halide complexes, trimethylammonium ion-pairs, and saccharides.
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Affiliation(s)
- Dong-Hao Li
- Department of Chemistry and Biochemistry, University of Notre Dame, 236 Nieuwland Science Hall, Notre Dame, Indiana 46556, United States
| | - Bradley D Smith
- Department of Chemistry and Biochemistry, University of Notre Dame, 236 Nieuwland Science Hall, Notre Dame, Indiana 46556, United States
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[2]Rotaxanes Bearing a Tetralactam Macrocycle: The Role of a Trifurcated Hydrogen Bond in the Crystalline State. European J Org Chem 2019. [DOI: 10.1002/ejoc.201900216] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Martinez-Cuezva A, Morales F, Marley GR, Lopez-Lopez A, Martinez-Costa JC, Bautista D, Alajarin M, Berna J. Thermally and Photochemically Induced Dethreading of Fumaramide-Based Kinetically Stable Pseudo[2]rotaxanes. European J Org Chem 2019. [DOI: 10.1002/ejoc.201900073] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Alberto Martinez-Cuezva
- Departamento de Química Orgánica; Facultad de Química; Regional Campus of International Excellence “Campus Mare Nostrum”; Universidad de Murcia; 30100 Murcia Spain
| | - Fatima Morales
- Departamento de Química Orgánica; Facultad de Química; Regional Campus of International Excellence “Campus Mare Nostrum”; Universidad de Murcia; 30100 Murcia Spain
| | - Grace R. Marley
- Departamento de Química Orgánica; Facultad de Química; Regional Campus of International Excellence “Campus Mare Nostrum”; Universidad de Murcia; 30100 Murcia Spain
| | - Adrian Lopez-Lopez
- Departamento de Química Orgánica; Facultad de Química; Regional Campus of International Excellence “Campus Mare Nostrum”; Universidad de Murcia; 30100 Murcia Spain
| | - Juan Carlos Martinez-Costa
- Departamento de Química Orgánica; Facultad de Química; Regional Campus of International Excellence “Campus Mare Nostrum”; Universidad de Murcia; 30100 Murcia Spain
| | | | - Mateo Alajarin
- Departamento de Química Orgánica; Facultad de Química; Regional Campus of International Excellence “Campus Mare Nostrum”; Universidad de Murcia; 30100 Murcia Spain
| | - Jose Berna
- Departamento de Química Orgánica; Facultad de Química; Regional Campus of International Excellence “Campus Mare Nostrum”; Universidad de Murcia; 30100 Murcia Spain
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