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Becerra D, Klotz AR, Hall LM. Single-molecule analysis of solvent-responsive mechanically interlocked ring polymers and the effects of nanoconfinement from coarse-grained simulations. J Chem Phys 2024; 160:114906. [PMID: 38511659 DOI: 10.1063/5.0191295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 03/02/2024] [Indexed: 03/22/2024] Open
Abstract
In this study, we simulate mechanically interlocked semiflexible ring polymers inspired by the minicircles of kinetoplast DNA (kDNA) networks. Using coarse-grained molecular dynamics simulations, we investigate the impact of molecular topological linkage and nanoconfinement on the conformational properties of two- and three-ring polymer systems in varying solvent qualities. Under good-quality solvents, for two-ring systems, a higher number of crossing points lead to a more internally constrained structure, reducing their mean radius of gyration. In contrast, three-ring systems, which all had the same crossing number, exhibited more similar sizes. In unfavorable solvents, structures collapse, forming compact configurations with increased contacts. The morphological diversity of structures primarily arises from topological linkage rather than the number of rings. In three-ring systems with different topological conformations, structural uniformity varies based on link types. Extreme confinement induces isotropic and extended conformations for catenated polymers, aligning with experimental results for kDNA networks and influencing the crossing number and overall shape. Finally, the flat-to-collapse transition in extreme confinement occurs earlier (at relatively better solvent conditions) compared to non-confined systems. This study offers valuable insights into the conformational behavior of mechanically interlocked ring polymers, highlighting challenges in extrapolating single-molecule analyses to larger networks such as kDNA.
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Affiliation(s)
- Diego Becerra
- William G. Lowrie Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, Ohio 43210, USA
| | - Alexander R Klotz
- Department of Physics and Astronomy, California State University, Long Beach, California 90840, USA
| | - Lisa M Hall
- William G. Lowrie Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, Ohio 43210, USA
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2
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Yang Z, Wu J, Li K, Zhou X, Lu D, Zhang L. Sliding Dynamics of a Small Charged Ring Chain on the Diblock Polyelectrolyte in Poly[2]catenane in the Presence of Counterions. J Phys Chem B 2023; 127:10189-10200. [PMID: 37734004 DOI: 10.1021/acs.jpcb.3c04107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/23/2023]
Abstract
In this study, we investigate the sliding dynamics of small charged ring chains along the rigid central cyclic diblock polyelectrolyte of AnBn in radial charged poly[2]catenane in the presence of counterions using molecular dynamics simulations and the Lifson-Jackson formula, and our aim is to study the effects of electrostatical interaction strength, the size of the charged small ring chain, and the rigid block length of the diblock polyelectrolyte on the sliding dynamics of a small ring chain threaded on the rigid diblock polyelectrolyte. The mean-square displacement g3(t) of a small ring chain sliding along the rigid diblock polyelectrolyte of A10B10 exhibits oscillating behavior at short time scales for the moderate electrostatical interaction strength, while for the weak or strong electrostatic interactions, it is normal subdiffusion at short time scales. For n = 1, the diffusion coefficient D of the small ring chain sliding along the rigid diblock polyelectrolyte of A1B1 decreases monotonically as the relative electrostatic interaction strength A increases from A = 0.25-4. However, for n ≠ 1, the diffusion coefficient D of the small ring chain sliding along the rigid diblock polyelectrolyte of AnBn first decreases and then increases with the increase of A, and the nonmonotonous relationship between D and A becomes more obvious for larger n. In view of the free energy potential, the sliding diffusion of a small ring chain is governed by both the width of the free energy potential well and the height of the free energy potential barrier. According to the potential of mean force (PMF) of the small ring chain sliding along the rigid diblock polyelectrolyte, we find that our results are in good agreement with the theoretical analysis using the Lifson-Jackson formula. These results may help us to understand the diffusion motion of a ring chain in radial poly[n]catenanes from a fundamental point of view and control the sliding dynamics in molecular designs.
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Affiliation(s)
- Zhiyong Yang
- Department of Physics, Jiangxi Agricultural University, Nanchang 330045, China
| | - Jiaxin Wu
- Department of Physics, Zhejiang University, Hangzhou 310027, China
| | - Ke Li
- College of Electronic and Information Engineering, Shanghai University of Electric Power, Shanghai 200090, China
| | - Xiaolin Zhou
- College of Physics and Optoelectronic Engineering, Harbin Engineering University, Harbin 150001, China
| | - Dan Lu
- Department of Physics, Jiangxi Agricultural University, Nanchang 330045, China
| | - Linxi Zhang
- Department of Physics, Zhejiang University, Hangzhou 310027, China
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Rheaume SN, Klotz AR. Nanopore translocation of topologically linked DNA catenanes. Phys Rev E 2023; 107:024504. [PMID: 36932513 DOI: 10.1103/physreve.107.024504] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 02/09/2023] [Indexed: 06/18/2023]
Abstract
The electrical signal associated with a biopolymer translocating through a nanoscale pore depends on the size, topology, and configuration of each molecule. Building upon recent interest in using solid-state nanopores for studying the topology of knotted and supercoiled DNA, we present experimental observations of topologically linked catenanes translocating through a solid-state nanopore. Using restriction enzymes, linked circular molecules were isolated from the mitochondrial DNA of Crithidia fasciculata, a structure known as a kinetoplast that comprises thousands of topologically interlocked minicircles. Digested kinetoplasts produce a spectrum of catenane topologies, which are identified from their nanopore translocation signals by spikes in the blockade current associated with the topological linkages. We attribute the different patterns of the measured electrical signals to 2-catenanes, linear and triangular 3-catenanes, and several types of 4- and 5-catenanes as well as more complex structures. Measurements of the translocation time of signals consistent with 2- and 3-catenanes suggest that topological friction between the linkages and the pore slows the translocation time of these structures, as predicted in recent simulations.
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Affiliation(s)
- Sierra N Rheaume
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Alexander R Klotz
- Department of Physics and Astronomy, California State University, Long Beach, Long Beach, California 90815, USA
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Topological Catenation Enhances Elastic Modulus of Single Linear Polycatenane. CHINESE JOURNAL OF POLYMER SCIENCE 2023. [DOI: 10.1007/s10118-023-2902-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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Li J, Zhang B, Li Y. Glass Formation in Mechanically Interlocked Ring Polymers: The Role of Induced Chain Stiffness. Macromolecules 2023. [DOI: 10.1021/acs.macromol.2c01368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Jian Li
- Department of Physics and Electronic Engineering, Heze University, Heze274015, China
| | - Bokai Zhang
- School of Physical Science and Technology, Southwest University, Chongqing400715, China
- Department of Physics, Zhejiang Sci-Tech University, Hangzhou310018, China
| | - Yushan Li
- Department of Physics and Electronic Engineering, Heze University, Heze274015, China
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Hagita K, Murashima T, Sakata N, Shimokawa K, Deguchi T, Uehara E, Fujiwara S. Molecular Dynamics of Topological Barriers on the Crystallization Behavior of Ring Polyethylene Melts with Trefoil Knots. Macromolecules 2022. [DOI: 10.1021/acs.macromol.2c01843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Katsumi Hagita
- Department of Applied Physics, National Defense Academy, 1-10-20, Hashirimizu, Yokosuka239-8686, Japan
| | - Takahiro Murashima
- Department of Physics, Tohoku University, 6-3, Aramaki-aza-Aoba, Aoba-ku, Sendai980-8578, Japan
| | - Naoki Sakata
- Department of Mathematics, Saitama University, 255, Shimo-Okubo, Sakura-ku, Saitama338-8570, Japan
- Department of Physics, Ochanomizu University, 2-1-1, Otsuka, Bunkyo-ku, Tokyo112-8610, Japan
| | - Koya Shimokawa
- Department of Mathematics, Saitama University, 255, Shimo-Okubo, Sakura-ku, Saitama338-8570, Japan
- Department of Mathematics, Ochanomizu University, 2-1-1, Otsuka, Bunkyo-ku, Tokyo112-8610, Japan
| | - Tetsuo Deguchi
- Department of Physics, Ochanomizu University, 2-1-1, Otsuka, Bunkyo-ku, Tokyo112-8610, Japan
| | - Erica Uehara
- Department of Physics, Ochanomizu University, 2-1-1, Otsuka, Bunkyo-ku, Tokyo112-8610, Japan
| | - Susumu Fujiwara
- Faculty of Materials Science and Engineering, Kyoto Institute of Technology, Matsugasaki,
Sakyo-ku, Kyoto606-8585, Japan
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Li D, Feng L, Tang Y, Zhu C. Entanglement Characteristic Time from Complex Moduli via i-Rheo GT. Polymers (Basel) 2022; 14:polym14235208. [PMID: 36501603 PMCID: PMC9740520 DOI: 10.3390/polym14235208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 11/11/2022] [Accepted: 11/13/2022] [Indexed: 12/03/2022] Open
Abstract
Tassieri et al. have introduced a novel rheological tool called "i-Rheo GT" that allows the evaluation of the frequency-dependent materials' linear viscoelastic properties from a direct Fourier transform of the time-dependent relaxation modulus G(t), without artifacts. They adopted i-Rheo GT to exploit the information embedded in G(t) derived from molecular dynamics simulations of atomistic and quasi-atomistic models, and they estimated the polymers' entanglement characteristic time (τe) from the crossover point of the moduli at intermediate times, which had never been possible before because of the poor fitting performance, at short time scales, of the commonly used generalized Maxwell models. Here, we highlight that the values of τe reported by Tassieri et al. are significantly different (i.e., an order of magnitude smaller) from those reported in the literature, obtained from either experiments or molecular dynamics simulations of different observables. In this work, we demonstrate that consistent values of τe can be achieved if the initial values of G(t), i.e., those governed by the bond-oscillation dynamics, are discarded. These findings have been corroborated by adopting i-Rheo GT to Fourier transform the outcomes of three different molecular dynamics simulations based on the following three models: a dissipative particle dynamics model, a Kremer-Grest model, and an atomistic polyethylene model. Moreover, we have investigated the variations of τe as function of (i) the 'cadence' at which G(t) is evaluated, (ii) the spring constant of the atomic bone, and (iii) the initial value of the shear relaxation modulus G(O). The ensemble of these results confirms the effectiveness of i-Rheo GT and provide new insights into the interpretation of molecular dynamics simulations for a better understanding of polymer dynamics.
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Murashima T, Hagita K, Kawakatsu T. Topological Transition in Multicyclic Chains with Structural Symmetry Inducing Stress-Overshoot Phenomena in Multicyclic/Linear Blends under Biaxial Elongational Flow. Macromolecules 2022. [DOI: 10.1021/acs.macromol.2c01579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Takahiro Murashima
- Department of Physics, Tohoku University, 6-3 Aramaki-aza-Aoba, Aoba-ku, Sendai980-8578, Japan
| | - Katsumi Hagita
- Department of Applied Physics, National Defense Academy, 1-10-20 Hashirimizu, Yokosuka239-8686, Japan
| | - Toshihiro Kawakatsu
- Department of Physics, Tohoku University, 6-3 Aramaki-aza-Aoba, Aoba-ku, Sendai980-8578, Japan
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Liu G, Rauscher PM, Rawe BW, Tranquilli MM, Rowan SJ. Polycatenanes: synthesis, characterization, and physical understanding. Chem Soc Rev 2022; 51:4928-4948. [PMID: 35611843 DOI: 10.1039/d2cs00256f] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Chemical composition and architecture are two key factors that control the physical and material properties of polymers. Some of the more unusual and intriguing polymer architectures are the polycatenanes, which are a class of polymers that contain mechanically interlocked rings. Since the development of high yielding synthetic routes to catenanes, there has been an interest in accessing their polymeric counterparts, primarily on account of the unique conformations and degrees of freedom offered by non-bonded interlocked rings. This has lead to the synthesis of a wide variety of polycatenane architectures and to studies aimed at developing structure-property relationships of these interesting materials. In this review, we provide an overview of the field of polycatenanes, exploring synthesis, architecture, properties, simulation, and modelling, with a specific focus on some of the more recent developments.
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Affiliation(s)
- Guancen Liu
- Department of Chemistry, University of Chicago, Chicago, IL, USA.
| | - Phillip M Rauscher
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL, USA
| | - Benjamin W Rawe
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL, USA
| | | | - Stuart J Rowan
- Department of Chemistry, University of Chicago, Chicago, IL, USA. .,Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL, USA.,Chemical and Engineering Sciences, Argonne National Laboratory, Lemont, IL, USA
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Hertzog JE, Maddi VJ, Hart LF, Rawe BW, Rauscher PM, Herbert KM, Bruckner EP, de Pablo JJ, Rowan SJ. Metastable doubly threaded [3]rotaxanes with a large macrocycle. Chem Sci 2022; 13:5333-5344. [PMID: 35655545 PMCID: PMC9093191 DOI: 10.1039/d2sc01486f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Accepted: 04/13/2022] [Indexed: 11/21/2022] Open
Abstract
Ring size is a critically important parameter in many interlocked molecules as it directly impacts many of the unique molecular motions that they exhibit. Reported herein are studies using one of the largest macrocycles reported to date to synthesize doubly threaded [3]rotaxanes. A large ditopic 46 atom macrocycle containing two 2,6-bis(N-alkyl-benzimidazolyl)pyridine ligands has been used to synthesize several metastable doubly threaded [3]rotaxanes in high yield (65-75% isolated) via metal templating. Macrocycle and linear thread components were synthesized and self-assembled upon addition of iron(ii) ions to form the doubly threaded pseudo[3]rotaxanes that could be subsequently stoppered using azide-alkyne cycloaddition chemistry. Following demetallation with base, these doubly threaded [3]rotaxanes were fully characterized utilizing a variety of NMR spectroscopy, mass spectrometry, size-exclusion chromatography, and all-atom simulation techniques. Critical to the success of accessing a metastable [3]rotaxane with such a large macrocycle was the nature of the stopper group employed. By varying the size of the stopper group it was possible to access metastable [3]rotaxanes with stabilities in deuterated chloroform ranging from a half-life of <1 minute to ca. 6 months at room temperature potentially opening the door to interlocked materials with controllable degradation rates.
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Affiliation(s)
- Jerald E Hertzog
- Department of Chemistry, University of Chicago Chicago IL 60637 USA
| | - Vincent J Maddi
- Department of Chemistry, University of Chicago Chicago IL 60637 USA
| | - Laura F Hart
- Pritzker School of Molecular Engineering, University of Chicago Chicago IL 60637 USA
| | - Benjamin W Rawe
- Pritzker School of Molecular Engineering, University of Chicago Chicago IL 60637 USA
| | - Phillip M Rauscher
- Pritzker School of Molecular Engineering, University of Chicago Chicago IL 60637 USA
| | - Katie M Herbert
- Pritzker School of Molecular Engineering, University of Chicago Chicago IL 60637 USA
- Department of Macromolecular Science and Engineering, Case Western Reserve University 2100 Adelbert Road Cleveland OH 44106 USA
| | - Eric P Bruckner
- Department of Macromolecular Science and Engineering, Case Western Reserve University 2100 Adelbert Road Cleveland OH 44106 USA
| | - Juan J de Pablo
- Pritzker School of Molecular Engineering, University of Chicago Chicago IL 60637 USA
- Chemical Science and Engineering Division and Center for Molecular Engineering, Argonne National Laboratory 9700 S. Cass Ave., Lemont IL 60434 USA
| | - Stuart J Rowan
- Department of Chemistry, University of Chicago Chicago IL 60637 USA
- Pritzker School of Molecular Engineering, University of Chicago Chicago IL 60637 USA
- Department of Macromolecular Science and Engineering, Case Western Reserve University 2100 Adelbert Road Cleveland OH 44106 USA
- Chemical Science and Engineering Division and Center for Molecular Engineering, Argonne National Laboratory 9700 S. Cass Ave., Lemont IL 60434 USA
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