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Zhang M, Nixon R, Schaufelberger F, Pirvu L, De Bo G, Leigh DA. Mechanical scission of a knotted polymer. Nat Chem 2024:10.1038/s41557-024-01510-3. [PMID: 38649468 DOI: 10.1038/s41557-024-01510-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Accepted: 03/18/2024] [Indexed: 04/25/2024]
Abstract
Molecular knots and entanglements form randomly and spontaneously in both biological and synthetic polymer chains. It is known that macroscopic materials, such as ropes, are substantially weakened by the presence of knots, but until now it has been unclear whether similar behaviour occurs on a molecular level. Here we show that the presence of a well-defined overhand knot in a polymer chain substantially increases the rate of scission of the polymer under tension (≥2.6× faster) in solution, because deformation of the polymer backbone induced by the tightening knot activates otherwise unreactive covalent bonds. The fragments formed upon severing of the knotted chain differ from those that arise from cleavage of a similar, but unknotted, polymer. Our solution studies provide experimental evidence that knotting can contribute to higher mechanical scission rates of polymers. It also demonstrates that entanglement design can be used to generate mechanophores that are among the most reactive described to date, providing opportunities to increase the reactivity of otherwise inert functional groups.
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Affiliation(s)
- Min Zhang
- School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, China
- Department of Chemistry, University of Manchester, Manchester, UK
| | - Robert Nixon
- Department of Chemistry, University of Manchester, Manchester, UK
| | | | - Lucian Pirvu
- Department of Chemistry, University of Manchester, Manchester, UK
| | - Guillaume De Bo
- Department of Chemistry, University of Manchester, Manchester, UK.
| | - David A Leigh
- School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, China.
- Department of Chemistry, University of Manchester, Manchester, UK.
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2
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Harawa V, Thorpe TW, Marshall JR, Sangster JJ, Gilio AK, Pirvu L, Heath RS, Angelastro A, Finnigan JD, Charnock SJ, Nafie JW, Grogan G, Whitehead RC, Turner NJ. Synthesis of Stereoenriched Piperidines via Chemo-Enzymatic Dearomatization of Activated Pyridines. J Am Chem Soc 2022; 144:21088-21095. [DOI: 10.1021/jacs.2c07143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Vanessa Harawa
- Department of Chemistry, University of Manchester, Manchester Institute of Biotechnology, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Thomas W. Thorpe
- Department of Chemistry, University of Manchester, Manchester Institute of Biotechnology, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - James R. Marshall
- Department of Chemistry, University of Manchester, Manchester Institute of Biotechnology, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Jack J. Sangster
- Department of Chemistry, University of Manchester, Manchester Institute of Biotechnology, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Amelia K. Gilio
- Department of Chemistry, University of York, Heslington, York YO10 5DD, United Kingdom
| | - Lucian Pirvu
- Department of Chemistry, University of Manchester, Manchester Institute of Biotechnology, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Rachel S. Heath
- Department of Chemistry, University of Manchester, Manchester Institute of Biotechnology, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Antonio Angelastro
- Department of Chemistry, University of Manchester, Manchester Institute of Biotechnology, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - James D. Finnigan
- Prozomix, Building 4, West End Ind. Estate, Haltwhistle NE49 9HA, United Kingdom
| | - Simon J. Charnock
- Prozomix, Building 4, West End Ind. Estate, Haltwhistle NE49 9HA, United Kingdom
| | - Jordan W. Nafie
- BioTools, Inc., 17546 Bee Line Highway, Jupiter, Florida 33478, United States
| | - Gideon Grogan
- Department of Chemistry, University of York, Heslington, York YO10 5DD, United Kingdom
| | - Roger C. Whitehead
- Department of Chemistry, University of Manchester, Manchester Institute of Biotechnology, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Nicholas J. Turner
- Department of Chemistry, University of Manchester, Manchester Institute of Biotechnology, 131 Princess Street, Manchester M1 7DN, United Kingdom
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3
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Abstract
Entangling strands in a well-ordered manner can produce useful effects, from shoelaces and fishing nets to brown paper packages tied up with strings. At the nanoscale, non-crystalline polymer chains of sufficient length and flexibility randomly form tangled mixtures containing open knots of different sizes, shapes and complexity. However, discrete molecular knots of precise topology can also be obtained by controlling the number, sequence and stereochemistry of strand crossings: orderly molecular entanglements. During the last decade, substantial progress in the nascent field of molecular nanotopology has been made, with general synthetic strategies and new knotting motifs introduced, along with insights into the properties and functions of ordered tangle sequences. Conformational restrictions imparted by knotting can induce allostery, strong and selective anion binding, catalytic activity, lead to effective chiral expression across length scales, binding modes in conformations efficacious for drug delivery, and facilitate mechanical function at the molecular level. As complex molecular topologies become increasingly synthetically accessible they have the potential to play a significant role in molecular and materials design strategies. We highlight particular examples of molecular knots to illustrate why these are a few of our favourite things.
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Affiliation(s)
- Zoe Ashbridge
- Department of Chemistry, The University of Manchester, Manchester, UK
| | | | - David A Leigh
- Department of Chemistry, The University of Manchester, Manchester, UK
- School of Chemistry and Molecular Engineering, East China Normal University, 3663 N Zhongshan Road, Shanghai, China
| | - Lucian Pirvu
- Department of Chemistry, The University of Manchester, Manchester, UK
| | | | - Liang Zhang
- Department of Chemistry, The University of Manchester, Manchester, UK
- School of Chemistry and Molecular Engineering, East China Normal University, 3663 N Zhongshan Road, Shanghai, China
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4
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Ashbridge Z, Knapp OM, Kreidt E, Leigh DA, Pirvu L, Schaufelberger F. Social Self-Sorting Synthesis of Molecular Knots. J Am Chem Soc 2022; 144:17232-17240. [PMID: 36067448 PMCID: PMC9501921 DOI: 10.1021/jacs.2c07682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
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We report the synthesis of molecular prime and composite
knots
by social self-sorting of 2,6-pyridinedicarboxamide (pdc) ligands
of differing topicity and stereochemistry. Upon mixing achiral monotopic
and ditopic pdc-ligand strands in a 1:1:1 ratio with Lu(III), a well-defined
heteromeric complex featuring one of each ligand strand and the metal
ion is selectively formed. Introducing point-chiral centers into the
ligands leads to single-sense helical stereochemistry of the resulting
coordination complex. Covalent capture of the entangled structure
by ring-closing olefin metathesis then gives a socially self-sorted
trefoil knot of single topological handedness. In a related manner,
a heteromeric molecular granny knot (a six-crossing composite knot
featuring two trefoil tangles of the same handedness) was assembled
from social self-sorting of ditopic and tetratopic multi-pdc strands.
A molecular square knot (a six-crossing composite knot of two trefoil
tangles of opposite handedness) was assembled by social self-sorting
of a ditopic pdc strand with four (S)-centers and
a tetratopic strand with two (S)- and six (R)-centers. Each of the entangled structures was characterized
by 1H and 13C NMR spectroscopy, mass spectrometry,
and circular dichroism spectroscopy. The precise control of composition
and topological chirality through social self-sorting enables the
rapid assembly of well-defined sequences of entanglements for molecular
knots.
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Affiliation(s)
- Zoe Ashbridge
- Department of Chemistry, University of Manchester, Manchester M13 9PL, U.K
| | - Olivia M Knapp
- Department of Chemistry, University of Manchester, Manchester M13 9PL, U.K
| | - Elisabeth Kreidt
- Department of Chemistry, University of Manchester, Manchester M13 9PL, U.K
| | - David A Leigh
- Department of Chemistry, University of Manchester, Manchester M13 9PL, U.K.,School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
| | - Lucian Pirvu
- Department of Chemistry, University of Manchester, Manchester M13 9PL, U.K
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5
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Abstract
Molecular knots are often prepared using metal helicates to cross the strands. We found that coordinatively mismatching oligodentate ligands and metal ions provides a more effective way to synthesize larger knots using Vernier templating. Strands composed of different numbers of tridentate 2,6-pyridinedicarboxamide groups fold around nine-coordinate lanthanide (III) ions to generate strand-entangled complexes with the lowest common multiple of coordination sites for the ligand strands and metal ions. Ring-closing olefin metathesis then completes the knots. A 3:2 (ditopic strand:metal) Vernier assembly produces +31#+31 and -31#-31 granny knots. Vernier complexes of 3:4 (tetratopic strand:metal) stoichiometry selectively form a 378-atom-long trefoil-of-trefoils triskelion knot with 12 alternating strand crossings or, by using opposing stereochemistry at the terminus of the strand, an inverted-core triskelion knot with six alternating and six nonalternating strand crossings.
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Affiliation(s)
- Zoe Ashbridge
- Department of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL, UK
| | - Elisabeth Kreidt
- Department of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL, UK
| | - Lucian Pirvu
- Department of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL, UK
| | | | - Joakim Halldin Stenlid
- SUNCAT Center for Interface Science and Catalysis, Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA.,SUNCAT Center for Interface Science and Catalysis, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Frank Abild-Pedersen
- SUNCAT Center for Interface Science and Catalysis, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - David A Leigh
- Department of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL, UK.,School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
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Song Y, Schaufelberger F, Ashbridge Z, Pirvu L, Vitorica-Yrezabal IJ, Leigh DA. Effects of turn-structure on folding and entanglement in artificial molecular overhand knots. Chem Sci 2020; 12:1826-1833. [PMID: 34163946 PMCID: PMC8179330 DOI: 10.1039/d0sc05897a] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
The length and constitution of spacers linking three 2,6-pyridinedicarboxamide units in a molecular strand influence the tightness of the resulting overhand (open-trefoil) knot that the strand folds into in the presence of lanthanide(iii) ions. The use of β-hairpin forming motifs as linkers enables a metal-coordinated pseudopeptide with a knotted tertiary structure to be generated. The resulting pseudopeptide knot has one of the highest backbone-to-crossing ratios (BCR)—a measure of knot tightness (a high value corresponding to looseness)—for a synthetic molecular knot to date. Preorganization in the crossing-free turn section of the knot affects aromatic stacking interactions close to the crossing region. The metal-coordinated pseudopeptide knot is compared to overhand knots with other linkers of varying tightness and turn preorganization, and the entangled architectures characterized by NMR spectroscopy, ESI-MS, CD spectroscopy and, in one case, X-ray crystallography. The results show how it is possible to program specific conformational properties into different key regions of synthetic molecular knots, opening the way to systems where knotting can be systematically incorporated into peptide-like chains through design. Spacers linking 2,6-pyridinedicarboxamide units influence the tightness of the corresponding lanthanide-coordinated overhand knot. β-Hairpin forming motifs generate a metal-coordinated pseudopeptide with a knotted tertiary structure.![]()
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Affiliation(s)
- Yiwei Song
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University Shanghai 200062 PR China
| | | | - Zoe Ashbridge
- Department of Chemistry, University of Manchester Oxford Road Manchester M13 9PL UK
| | - Lucian Pirvu
- Department of Chemistry, University of Manchester Oxford Road Manchester M13 9PL UK
| | | | - David A Leigh
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University Shanghai 200062 PR China .,Department of Chemistry, University of Manchester Oxford Road Manchester M13 9PL UK
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7
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Katsonis N, Lancia F, Leigh DA, Pirvu L, Ryabchun A, Schaufelberger F. Knotting a molecular strand can invert macroscopic effects of chirality. Nat Chem 2020; 12:939-944. [DOI: 10.1038/s41557-020-0517-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 06/25/2020] [Indexed: 11/10/2022]
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8
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Abstract
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We
report on the stereoselective synthesis of both molecular granny
and square knots through the use of lanthanide-complexed overhand
knots of specific handedness as three-crossing “entanglement
synthons”. The composite knots are assembled by combining two
entanglement synthons (of the same chirality for a granny knot; of
opposite handedness for a square knot) in three synthetic steps: first,
a CuAAC reaction joins together one end of each overhand knot. Ring-closing
olefin metathesis (RCM) then affords the closed-loop knot, locking
the topology. This allows the lanthanide ions necessary for stabilizing
the entangled conformation of the synthons to subsequently be removed.
The composite knots were characterized by 1H and 13C NMR spectroscopy and mass spectrometry and the chirality of the
knot stereoisomers compared by circular dichroism. The synthetic strategy
of combining building blocks of defined stereochemistry (here overhand
knots of Λ- or Δ-handed entanglement) is reminiscent of
the chiron approach of using minimalist chiral synthons in the stereoselective
synthesis of molecules with multiple asymmetric centers.
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Affiliation(s)
- David A Leigh
- School of Chemistry , University of Manchester , Oxford Road , Manchester M13 9PL , U.K
| | - Lucian Pirvu
- School of Chemistry , University of Manchester , Oxford Road , Manchester M13 9PL , U.K
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9
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Abstract
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The binding of Zn(II) cations to
a pentafoil (51) knotted
ligand allows the synthesis of otherwise inaccessible metalated molecular
pentafoil knots via transmetalation, affording the corresponding “first-sphere”
coordination Co(II), Ni(II), and Cu(II) pentanuclear knots in good
yields (≥85%). Each of the knot complexes was characterized
by mass spectrometry, the diamagnetic (zinc) knot complex was characterized
by 1H and 13C NMR spectroscopy, and the zinc,
cobalt, and nickel pentafoil knots afforded single crystals whose
structures were determined by X-ray crystallography. Lehn-type circular
helicates generally only form with tris-bipy ligand strands and Fe(II)
(and, in some cases, Ni(II) and Zn(II)) salts, so such architectures
become accessible for other metal cations only through the use of
knotted ligands. The different metalated knots all exhibit “second-sphere”
coordination of a single chloride ion within the central cavity of
the knot through CH···Cl– hydrogen
bonding and electrostatic interactions. The chloride binding affinities
were determined in MeCN by isothermal titration calorimetry, and the
strength of binding was shown to vary over 3 orders of magnitude for
the different metal-ion–knotted-ligand second-sphere coordination
complexes.
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Affiliation(s)
- Liang Zhang
- School of Chemistry and Molecular Engineering , East China Normal University , Shanghai 200062 , China.,School of Chemistry , University of Manchester , Manchester M13 9PL , United Kingdom
| | - Alexander J Stephens
- School of Chemistry , University of Manchester , Manchester M13 9PL , United Kingdom
| | | | - Lucian Pirvu
- School of Chemistry , University of Manchester , Manchester M13 9PL , United Kingdom
| | | | - Christopher J Robinson
- SYNBIOCHEM, Manchester Institute of Biotechnology , University of Manchester , Manchester M1 7DN , United Kingdom
| | - David A Leigh
- School of Chemistry and Molecular Engineering , East China Normal University , Shanghai 200062 , China.,School of Chemistry , University of Manchester , Manchester M13 9PL , United Kingdom
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10
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Leigh DA, Pirvu L, Schaufelberger F, Tetlow DJ, Zhang L. Frontispiz: Securing a Supramolecular Architecture by Tying a Stopper Knot. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201883361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- David A. Leigh
- School of ChemistryUniversity of Manchester Oxford Road Manchester M13 9PL UK
| | - Lucian Pirvu
- School of ChemistryUniversity of Manchester Oxford Road Manchester M13 9PL UK
| | | | - Daniel J. Tetlow
- School of ChemistryUniversity of Manchester Oxford Road Manchester M13 9PL UK
| | - Liang Zhang
- School of ChemistryUniversity of Manchester Oxford Road Manchester M13 9PL UK
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11
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Leigh DA, Pirvu L, Schaufelberger F, Tetlow DJ, Zhang L. Frontispiece: Securing a Supramolecular Architecture by Tying a Stopper Knot. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/anie.201883361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- David A. Leigh
- School of ChemistryUniversity of Manchester Oxford Road Manchester M13 9PL UK
| | - Lucian Pirvu
- School of ChemistryUniversity of Manchester Oxford Road Manchester M13 9PL UK
| | | | - Daniel J. Tetlow
- School of ChemistryUniversity of Manchester Oxford Road Manchester M13 9PL UK
| | - Liang Zhang
- School of ChemistryUniversity of Manchester Oxford Road Manchester M13 9PL UK
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12
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Leigh DA, Pirvu L, Schaufelberger F, Tetlow DJ, Zhang L. Securing a Supramolecular Architecture by Tying a Stopper Knot. Angew Chem Int Ed Engl 2018; 57:10484-10488. [PMID: 29708636 PMCID: PMC6099318 DOI: 10.1002/anie.201803871] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2018] [Indexed: 11/11/2022]
Abstract
We report on a rotaxane-like architecture secured by the in situ tying of an overhand knot in the tris(2,6-pyridyldicarboxamide) region of the axle through complexation with a lanthanide ion (Lu3+ ). The increase in steric bulk caused by the knotting locks a crown ether onto the thread. Removal of the lutetium ion unties the knot, and when the axle binding site for the ring is deactivated, the macrocycle spontaneously dethreads. When the binding interaction is switched on again, the crown ether rethreads over the 10 nm length of the untangled strand. The overhand knot can be retied, relocking the threaded structure, by once again adding lutetium ions.
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Affiliation(s)
- David A. Leigh
- School of ChemistryUniversity of ManchesterOxford RoadManchesterM13 9PLUK
| | - Lucian Pirvu
- School of ChemistryUniversity of ManchesterOxford RoadManchesterM13 9PLUK
| | | | - Daniel J. Tetlow
- School of ChemistryUniversity of ManchesterOxford RoadManchesterM13 9PLUK
| | - Liang Zhang
- School of ChemistryUniversity of ManchesterOxford RoadManchesterM13 9PLUK
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13
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Affiliation(s)
- David A. Leigh
- School of ChemistryUniversity of Manchester Oxford Road Manchester M13 9PL UK
| | - Lucian Pirvu
- School of ChemistryUniversity of Manchester Oxford Road Manchester M13 9PL UK
| | | | - Daniel J. Tetlow
- School of ChemistryUniversity of Manchester Oxford Road Manchester M13 9PL UK
| | - Liang Zhang
- School of ChemistryUniversity of Manchester Oxford Road Manchester M13 9PL UK
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14
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Heard KWJ, Morrison JJ, Weston L, Lo CH, Pirvu L, Raftery J, Little MS, McDouall JJW, Yeates SG, Quayle P. An orthogonal C–H borylation – cross-coupling strategy for the preparation of tetrasubstituted “A2B2”-chrysene derivatives with tuneable photophysical properties. Chem Commun (Camb) 2015; 51:6115-8. [PMID: 25745672 DOI: 10.1039/c4cc10132d] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Cl-substituents serve as a functionalisable regiocontrol element for the orthogonal functionalisation of chrysene.
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Affiliation(s)
| | | | - L. Weston
- School of Chemistry
- University of Manchester
- Manchester
- UK
| | - C. H. Lo
- School of Chemistry
- University of Manchester
- Manchester
- UK
| | - L. Pirvu
- School of Chemistry
- University of Manchester
- Manchester
- UK
| | - J. Raftery
- School of Chemistry
- University of Manchester
- Manchester
- UK
| | - M. S. Little
- School of Chemistry
- University of Manchester
- Manchester
- UK
| | | | - S. G. Yeates
- School of Chemistry
- University of Manchester
- Manchester
- UK
| | - P. Quayle
- School of Chemistry
- University of Manchester
- Manchester
- UK
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