Single-chain Level Research Articles

Multidimensional Decryption of Metallopolymer at Single-Chain Level

Multidimensional Decryption of Metallopolymer at Single-Chain Level

Characterization of single synthetic polymers via magnetic tweezers

AbstractDue to the ability to perform the parallel measurement of multiple single chains and exert precise control over stretching force in the sub‐nanonewton regime, magnetic tweezers (MT) are a suitable tool to study the individual chain conformations and inherent behaviors of polymers. Herein, we examined the applications of MT in studying single synthetic polymers, distinct from previous reviews focusing on biological polymers such as DNAs. We first presented an overview of the technical aspects of MT, including the imaging setup, the algorithm of three‐dimensional single particle tracking, the configuration of magnets, the calibration and control of magnetic forces, the assembly of flow cells, and the polymer tethering methods. Then, we discussed selected examples highlighting the utilization of MT in studying the chain conformation, mechanical properties, ion and ligands effect, regime transition mechanism, and polymerization dynamics of single synthetic polymers. We envision that MT can serve as a powerful toolbox for delving into the structure–property correlations at the single chain level, which provides quantitative validations for building the theoretical models of synthetic polymers. In the end, we contemplated potential avenues and opportunities for future research in this domain.

Role of Strong Localized vs Weak Distributed Interactions in Disordered Protein Phase Separation.

Interaction strength and localization are critical parameters controlling the single-chain and condensed-state properties of intrinsically disordered proteins (IDPs). Here, we decipher these relationships using coarse-grained heteropolymers comprised of hydrophobic (H) and polar (P) monomers as model IDPs. We systematically vary the fraction of P monomers XP and employ two distinct particle-based models that include either strong localized attractions between only H-H pairs (HP model) or weak distributed attractions between both H-H and H-P pairs (HP+ model). To compare different sequences and models, we first carefully tune the attraction strength for all sequences to match the single-chain radius of gyration. Interestingly, we find that this procedure produces similar conformational ensembles, nonbonded potential energies, and chain-level dynamics for single chains of almost all sequences in both models, with some deviations for the HP model at large XP. However, we observe a surprisingly rich phase behavior for the sequences in both models that deviates from the expectation that similarity at the single-chain level will translate to a similar phase-separation propensity. Coexistence between dilute and dense phases is only observed up to a model-dependent XP, despite the presence of favorable interchain interactions, which we quantify using the second virial coefficient. Instead, the limited number of attractive sites (H monomers) leads to the self-assembly of finite-sized clusters of different sizes depending on XP. Our findings strongly suggest that models with distributed interactions favor the formation of liquid-like condensates over a much larger range of sequence compositions compared to models with localized interactions.

Visualizing the Orientation of Single Polymers Induced by Spin-Coating.

The orientation of chains within polymeric materials influences their electrical, mechanical, and thermal properties. While many techniques can infer the orientation distribution of a bulk ensemble, it is challenging to determine this information at the single-chain level, particularly in an environment of otherwise identical polymers. Here, we use single-molecule localization microscopy (SMLM) to visualize the directions of chains within spin-coated polymer films. We find a strong relationship between shear force and the degree and direction of orientation, and additionally, we reveal the effects of chain length and solvent evaporation rate. This work utilizes single-chain resolution to observe the important, though often overlooked, property of chain orientation in the common fabrication process of spin-coating.

Force-induced hydrogen bonding between single polyformaldehyde chain and water

To explore the nature of water insolubility of polyformaldehyde (POM), we utilize single-molecule atomic force microscopy (AFM) and molecular dynamics (MD) simulations to study the possible interactions between POM and water at the single-chain level. Single-molecule force-extension curves of POM obtained in nonane and deionized water showed a marked deviation in the middle force region, which is similar to that observed in polyethylene glycol (PEG). The results indicate that force-induced hydrogen bonding between POM and water occurs upon initial stretching, followed by a dehydration process upon high force stretching. MD simulations show that POM chain itself is able to form H-bonds with water, but this potential is heavily hindered by the native conformation in the crystal. This finding not only provides new insight into the understanding of water insolubility of POM, but also helps the rational design of advanced polymer materials in the future.

Tip-enhanced Raman spectroscopy of confined carbon chains.

Long linear chains of carbon encapsulated in carbon nanotubes represent the finite realization of carbyne, the truly one-dimensional carbon allotrope. Driven by advances in the synthesis of such structures, carbyne has attracted significant interest in recent years, with numerous experimental studies exploring its remarkable properties. As for other carbon nanomaterials, Raman spectroscopy has played an important role in the characterization of carbyne. In particular, tip-enhanced Raman scattering (TERS) has enabled imaging and spectroscopy down to the single-chain level. In this article, we provide a general introduction to carbyne and discuss the principles and experimental implementation of TERS as a key technology for the investigation of this material system. Within this context, the development of optical nanoantennas as TERS probes is addressed. We then summarize the latest progress in the Raman spectroscopic characterization of confined carbyne, with a focus on the findings assisted by TERS. Finally, we discuss open questions in the field and outline how TERS can contribute to solving them in future studies.

Real-Time Monitoring of Formation and Dynamics of Intra- and Interchain Phases in Single Molecules of Polyfluorene.

Poly(9,9-dioctylfluorene) (PFO) is one of the most important conjugated polymer materials, exhibiting outstanding photophysical and electrical properties. PFO is also known for a diversity of morphological phases determined by conformational states of the main chain. Our goal in this work is to address some of the key questions on formation and dynamics of one such conformation, the β-phase, by following in real time the evolution of fluorescence spectra of single PFO chains. The PFO is dispersed in a thin polystyrene film, and the spectra are monitored during the process of solvent vapor annealing with toluene. We confirm unambiguously that the PFO β-phase segments are formed on a true single-chain level at room temperature in the solvent-softened polystyrene. We further find that the formation of the β-phase is a dynamic and reversible process occurring on the order of seconds, leading to repeated spontaneous transitions between the glassy and β-phase segments during the annealing. Comparison of PFO with two largely different molecular weights (Mw) shows that chains with lower Mw form the β-phase segments much faster. For the high Mw PFO chains, a detailed Franck-Condon analysis of the β-phase spectra shows a large distribution of the Huang-Rhys factor, S, and even dynamic changes of this factor occurring on a single chain. Such dynamics are likely a manifestation of changing coherence length of the exciton. Further, for the high Mw PFO chains we observe an additional conformational state, a crystalline γ-phase. The γ-phase formation is also a spontaneous reversible process in the solvent-softened matrix. The phase can form from both the β-phase and the glassy phase, and the formation requires high Mw to enable intersegment interactions in a self-folded chain.

Emerging trends in solution self-assembly of block copolymers

Since the foundation of macromolecular science by Staudinger, advances in polymer chemistry have unveiled enormous avenues for controlling chemical structures at the molecular scale. As a typical self-assembling polymer covalently linked by chemically distinct polymer blocks, amphiphilic block copolymers (BCPs) spontaneously form a variety of nanostructures with diverse functional applications, especially in the fields of nanomedicine and biomaterials. Self-assembling processes could occur at single chain level (i.e., intrachain folding) or involve multiple chains with similar and dissimilar chemical structures (i.e., interchain association). This review article discusses recent trends concerning solution self-assembly of BCPs, including the formation of inverted mesophases, self-folding into single-chain nanoparticles (SCNPs), compartmentalized nanoparticles with sophisticated functions, and nanostructures of amphiphilic copolymers with precise chain lengths and predetermined sequences, by highlighting selected examples.

Brachiation of a polymer chain in the presence of a dynamic network.

The viscoelastic behavior of a physically crosslinked gel involves a spectrum of molecular relaxation processes, which at the single-chain level involve the chain undergoing transient hand-to-hand motion through the network. We develop a self-consistent theory for describing transiently associating polymer solutions that captures these complex dynamics. A single polymer chain transiently binds to a viscoelastic background that represents the polymer network formed by surrounding polymer chains. The viscoelastic background is described in the equation of motion as a memory kernel, which is self-consistently determined based on the predicted rheological behavior from the chain itself. The solution to the memory kernel is translated into rheological predictions of the complex modulus over a wide range of frequencies to capture the time-dependent behavior of a physical gel. Using the loss tangent predictions, a phase diagram is shown for the sol-gel transition of polymers with dynamic association affinities. This theory provides a predictive, molecular-level framework for the design of associating gels and supramolecular assemblies with targeted rheological properties.

Roles of easy-plane and easy-axis XXZ anisotropy and bond alternation in a frustrated ferromagnetic spin- 12 chain

The spin-$1/2$ Heisenberg chain with a ferromagnetic first-neighbor exchange coupling $J_1$ and an antiferromagnetic second-neighbor $J_2$ has a Haldane dimer ground state with an extremely small spin gap. Thus, the ground state is readily altered by perturbations. Here, we investigate the effects of XXZ exchange magnetic anisotropy of both the easy-axis and easy-plane types and an alternation in $J_1$ on the ground state, the spin gap, and magnetic properties of the frustrated ferromagnetic spin-$1/2$ chain. It is found that there are two distinct dimerized spin-gap phases, in one of which the spin gap and the magnetic susceptibility are extremely small around the SU(2) symmetric case and in the other they are moderately large far away from the SU(2) symmetric case. A small alternation in the amplitude of $J_1$ rapidly shortens the pitch of spin correlations towards the four-spin periodicity, as in the limit of $J_1/J_2\to0$. These effects are not sufficient to quantitatively explain overall experimentally observed magnetic properties in the quasi-one-dimensional spin-gapped magnetoelectric cuprate Rb$_2$Cu$_2$Mo$_3$O$_{12}$ that exhibits ferroelectricity stabilized by a magnetic field. Our results are also relevant to Cs$_2$Cu$_2$Mo$_3$O$_{12}$, where the ferromagnetic intrachain and antiferromagnetic interchain order has recently been found, in a single chain level. We also reveal the nature of symmetry-protected topological phase transitions in the model by mapping onto effective spin-1 chain models.

Modular decomposition of protein structure using community detection

As the number of solved protein structures increases, the opportunities for meta-analysis of this dataset increase too. Protein structures are known to be formed of domains; structural and functional subunits that are often repeated across sets of proteins. These domains generally form compact, globular regions, and are therefore often easily identifiable by inspection, yet the problem of automatically fragmenting the protein into these compact substructures remains computationally challenging. Existing domain classification methods focus on finding subregions of protein structure that are conserved, rather than finding a decomposition which spans the full protein structure. However, such a decomposition would find ready application in coarse-graining molecular dynamics, analysing the protein’s topology, in de novo protein design and in fitting electron microscopy maps. Here, we present a tool for performing this modular decomposition using the Infomap community detection algorithm. The protein structure is abstracted into a network in which its amino acids are the nodes, and where the edges are generated using a simple proximity test. Infomap can then be used to identify highly intra-connected regions of the protein. We perform this decomposition systematically across 4000 distinct protein structures, taken from the Protein Data Bank. The decomposition obtained correlates well with existing PFAM sequence classifications, but has the advantage of spanning the full protein, with the potential for novel domains. The coarse-grained network formed by the communities can also be used as a proxy for protein topology at the single-chain level; we demonstrate that grouping these proteins by their coarse-grained network results in a functionally significant classification.

Intrachain Aggregates as the Origin of Green Emission in Polyfluorene Studied on Ensemble and Single-Chain Level

Polyfluorenes are conjugated polymers that show strong blue emission and as such have been explored for potential applications in light-emitting devices. However, heat treatment, prolonged exposure...

Conformation and dynamics of single polymer chain studied by optical microscopy techniques beyond the diffraction limit.

The origin of the unique properties of a polymer material is the large entropic term of a single molecule, which has a chain-like structure with a large molecular weight. From the viewpoint of understanding the fundamental polymer physics, conformation of the single polymer chain is one of the most important matters; however, it has been difficult to examine the behavior of a single chain because of the limitation of conventional experimental methods. Recent developments in optical microscopy allow the fluorescence imaging beyond the diffraction limit of light, and the author's group showed that the conformation and the dynamics of a single polymer chain can be examined by the high-resolution fluorescence imaging. This review presents the application of optical microscopy with nanometric spatial resolution to study the polymer materials at the single-chain level.

Phase behavior of aqueous polyacrylic acid solutions using atomistic molecular dynamics simulations of model oligomers

We have performed fully atomistic molecular dynamics simulations of aqueous solutions of a weak, pH-responsive polyelectrolyte, polyacrylic acid (PAA). Model oligomers of PAA of different tacticities, molecular weights, degrees of deprotonation, and deprotonation patterns are simulated with water molecules. Deprotonation of PAA chains that occurs with an increase in pH results in an increase in Coulomb repulsion between chain segments on one hand, and a non-monotonic change in the hydrogen bonding between chain segments on the other hand. Consequently, at the single chain level, PAA chains are stretched at higher pH values, where the amount of stretching varies with chain tacticity. For the multiple chains case, PAA forms aggregates at higher concentrations, which are relatively denser and contain lesser water (solid-like) at lower pH than compared to higher pH (liquid-like). Such phase transitions of PAA aggregates with pH has possible implications in the design of pH-responsive polyelectrolytes for applications in drug delivery.

Hydrophilicities of amylose and natural cellulose are regulated by the linkage between sugar rings.

Comparative studies of single molecule force spectroscopy and molecular dynamics simulations indicate that natural cellulose is more hydrophobic than amylose at the single-chain level, implying that the hydrophobicities of these polymeric isomers are regulated by only one parameter in the chains, the linkage between the sugar rings.

Tip-enhanced Raman spectroscopy: plasmid-free vs. plasmid-embedded DNA

Tip-enhanced Raman spectroscopy (TERS) provides greatly enhanced Raman signals along with ultra-high lateral spatial resolutions and has been demonstrated to be a technique of choice to study a variety of biochemical specimens such as DNA and RNA at the single chain level. However, the sensitivity of TERS to demonstrate the influence of the nanoscale environment on DNA properties has not been investigated. Herein, we used a gap-mode TERS as an ultra-sensitive label-free technique to investigate the influence of the local plasmid on the DNA properties of a β2-adrenergic receptor (β2AR). Remarkable lateral spatial resolutions down to 8 nm were also acquired for the collected Raman signals under ambient conditions. This approach offers not only a tool to examine the influence of the local nanoscale environment surrounding the DNA structure, but also the localization of the majority of nucleic acid base(s) present in selected regions on the DNA strand.

Nanoscale Study of Polymer Dynamics.

The thermal motion of polymer chains in a crowded environment is anisotropic and highly confined. Whereas theoretical and experimental progress has been made, typically only indirect evidence of polymer dynamics is obtained either from scattering or mechanical response. Toward a complete understanding of the complicated polymer dynamics in crowded media such as biological cells, it is of great importance to unravel the role of heterogeneity and molecular individualism. In the present work, we investigate the dynamics of synthetic polymers and the tube-like motion of individual chains using time-resolved fluorescence microscopy. A single fluorescently labeled polymer molecule is observed in a sea of unlabeled polymers, giving access to not only the dynamics of the probe chain itself but also to that of the surrounding network. We demonstrate that it is possible to extract the characteristic time constants and length scales in one experiment, providing a detailed understanding of polymer dynamics at the single chain level. The quantitative agreement with bulk rheology measurements is promising for using local probes to study heterogeneity in complex, crowded systems.

The effect of covalently linked RGD peptide on the conformation of polysaccharides in aqueous solutions

Covalently modified polysaccharides are routinely used in tissue engineering due to their tailored biofunctionality. Understanding the effect of single-chain level modification on the solution conformation of the single chain, and more importantly on the self-assembly and aggregation of the ensemble of chains is expected to improve our ability to control network topology and the properties of the resulting gels. Attaching an RGD peptide to a polysaccharide backbone is a common procedure used to promote cell adhesion in hydrogel scaffolds. Recently it has been shown that the spatial presentation of the RGD sequences affects the cell behavior; thus, understanding the effects of grafted RGD on the conformational properties of the solvated polysaccharide chains is a prerequisite for rational design of polysaccharide-peptide based biomaterials. Here we investigate the effect of covalently linked G4RGDS on the conformational state of the individual chain and chain assemblies of alginate, chitosan, and hyaluronic acid (HA) in aqueous solutions. Two peptide fractions were studied using small-angle X-ray scattering (SAXS) and rheology. In all cases, upon peptide conjugation structural differences were observed. Analysis of the scattering data shows evidence of clustering for a higher fraction of bound peptide. Moreover for all three polysaccharides the typical shear thinning behavior of the natural polysaccharide solutions is replaced by a Newtonian fluid behavior for the lower fraction conjugated peptide while a more pronounced shear thinning behavior is observed for the higher fraction. These results indicate that the fraction of the bounded peptide, determines the behavior of a polysaccharide-peptide conjugates in solution, regardless of the specific nature of the polysaccharide.

Measuring the Confinement Free Energy and Effective Width of Single Polymer Chains via Single-Molecule Tetris

We perform single-molecule partitioning measurements of the free energy of chain confinement and self-exclusion as a function of confinement dimension and buffer ionic strength via single-molecule Tetris. Individual DNA chains, confined in a nanoslit with a lattice of embedded nanocavities, partition their contour between the cavities. Changes in device geometry and buffer chemistry lead to changes in the number of cavities occupied. We are able to deduce the confinement free energy difference between the nanocavities and the nanoslit by observing how the number of cavities occupied by a single chain varies as a function of device dimension. These measurements enable us to confirm theoretical predictions for confinement free energy based on worm-like chain formalism and quantify the chain effective width w, providing a direct measure of the size of excluded-volume effect on a single-chain level.

Revealing the Hydrophobicity of Natural Cellulose by Single-Molecule Experiments

Natural cellulose (NC) is the most abundant biomacromolecule. The fact that each pyranose ring of NC has three hydroxyl groups implies that NC should be highly hydrophilic. The paradoxical water insolubility of NC is usually explained by the strong tendency to form the hydrogen-bonding network by the high content of hydroxyl groups. In this study, we present the first experimental evidence that NC is rather hydrophobic, even if the chains are molecularly dispersed. By single-molecule force spectroscopy, the single-chain mechanics of NC has been studied in various liquid environments. In a common nonpolar solvent, octane, NC shows the elastic force–extension (F–E) curve. We find that this kind of F–E curve can be fitted well by the QM-FJC model, in which the single-chain elasticity obtained from quantum mechanical (QM) calculations is integrated into the freely jointed-chain (FJC) model. However, the result of NC obtained in water is different, which shows a long plateau in the F–E curve. Further study shows that the height of the plateau is temperature dependent. However, the plateau disappears when an 8 M urea solution is used as the liquid environment. AFM images obtained in water show that single NC chains exist in a compact globule conformation on the sample surface. According to the molecular structure, methylcellulose (MC) should be more hydrophobic than NC. However, no plateau can be observed from the MC samples in water. On the basis of all the results above, we can draw a conclusion that both of the hydrophobic effect and the crystallization of NC contribute to the plateau in the F–E curve obtained in water. The experimental observation of the hydrophobic nature of NC at the single-chain level provides new insights into the understanding of NC.