Interplay of Structure and Dynamics in Macromolecular and Supramolecular Systems

Single-exonuclease nanocircuits reveal the RNA degradation dynamics of PNPase and demonstrate potential for RNA sequencing

The degradation process of RNA is decisive in guaranteeing high-fidelity translation of genetic information in living organisms. However, visualizing the single-base degradation process in real time and deciphering the degradation mechanism at the single-enzyme level remain formidable challenges. Here, we present a reliable in-situ single-PNPase-molecule dynamic electrical detector based on silicon nanowire field-effect transistors with ultra-high temporal resolution. These devices are capable of realizing real-time and label-free monitoring of RNA analog degradation with single-base resolution, including RNA analog binding, single-nucleotide hydrolysis, and single-base movement. We discover a binding event of the enzyme (near the active site) with the nucleoside, offering a further understanding of the RNA degradation mechanism. Relying on systematic analyses of independent reads, approximately 80% accuracy in RNA nucleoside sequencing is achieved in a single testing process. This proof-of-concept sets up a Complementary Metal Oxide Semiconductor (CMOS)-compatible playground for the development of high-throughput detection technologies toward mechanistic exploration and single-molecule sequencing.

Triple-pulse excitation: An efficient way for suppressing background signals and eliminating radio-frequency acoustic ringing in direct polarization NMR experiments

Direct polarization using a single pulse is the simplest excitation scheme in nuclear magnetic resonance (NMR) experiments, capable of quantifying various compositions in many materials applications. However, this single-pulse excitation generally gives rise to NMR spectra with a severely distorted baseline due to the background signals arising from probe components and/or due to the radio-frequency (RF) acoustic ringing, especially in low-γ nuclei and wide-line NMR. In this work, a triple-pulse excitation scheme is proposed to simultaneously suppress the background signals and eliminate the RF acoustic ringing. The acoustic ringing is cancelled through subtraction in any two consecutive scans by alternating the receiver phase while keeping the phase of the pulse right before acquisition the same. While the triple-pulse scheme generates an additional flip-angle dependent scaling to the traditional single-pulse excitation profile in such a way that the scaling is one when the flip-angle is ∼90° but becomes almost zero when the flip-angle is very small. Therefore, the background signals arising from the materials outside the sample coil experiencing a very small fraction of the RF flip-angles can be effectively suppressed. Various samples containing ¹H and quadrupolar nuclei (¹⁷O, ²⁵Mg, and ²³Na) have been used to demonstrate the effectiveness of this newly proposed triple-pulse excitation in terms of suppressing the background signals and eliminating the acoustic ringing effects.

Advanced spectroscopy, microscopy, diffraction and thermal analysis of polyamide adhesives and prediction of their functional properties with solid-state NMR spectroscopy

Advanced spectroscopy, microscopy, diffraction and thermal analysis reveal heterogeneity and dynamics in polyamide industrial adhesives; solid-state NMR spectroscopy enable the prediction of their functional properties.

Irreversible adsorption of polymer melts and nanoconfinement effects

For almost a decade, growing experimental evidence has revealed a strong correlation between the properties of nanoconfined polymers and the number of chains irreversibly adsorbed onto nonrepulsive interfaces, e.g. the supporting substrate of thin polymer coatings, or nanofillers dispersed in polymer melts. Based on such a correlation, it has already been possible to tailor structural and dynamics properties - such as the glass transition temperature, the crystallization rate, the thermal expansion coefficients, the viscosity and the wettability - of nanomaterials by controlling the adsorption kinetics. This evidence indicates that irreversible adsorption affects nanoconfinement effects. More recently, also the opposite phenomenon was experimentally observed: nanoconfinement alters interfacial interactions and, consequently, also the number of chains adsorbed in equilibrium conditions. In this review we discuss this intriguing interplay between irreversible adsorption and nanoconfinement effects in ultrathin polymer films. After introducing the methods currently used to prepare adsorbed layers and to measure the number of irreversibly adsorbed chains, we analyze the models employed to describe the kinetics of adsorption in polymer melts. We then discuss the structure of adsorbed polymer layers, focusing on the complex macromolecular architecture of interfacial chains and on their thermal expansion; we examine the way in which the structure of the adsorbed layer affects the thermal glass transition temperature, vitrification, and crystallization. By analyzing segmental dynamics of 1D confined systems, we describe experiments to track the changes in density during adsorption. We conclude this review with an analysis of the impact of nanoconfinement on adsorption, and a perspective on future work where we also address the key ideas of irreversibility, equilibration and long-range interactions.

J(77 Se,1 H) and J(77 Se,13 C) couplings of seleno-carbohydrates obtained by 77 Se satellite 1D 13 C spectroscopy and 77 Se selective HR-HMBC spectroscopy

Seleno-carbohydrates are those in which the oxygen of the glycosidic bond or the hydroxyl group is artificially replaced with selenium. This substitution changes ¹ H and ¹³ C chemical shifts and produces spin coupling constants involving ⁷⁷ Se. Coupling constants, such as ^2-3 J(⁷⁷ Se, ¹ H), are likely to be useful for conformational analyses of glycans because such couplings are never observed in natural glycans. Several papers have discussed the relationship between ^2-3 J(⁷⁷ Se, ¹ H) and conformation; however, only few reports describe ^1-3 J(⁷⁷ Se, ¹³ C), which could also be useful. Here, we obtain ⁷⁷ Se coupling constants of seleno-carbohydrates from ⁷⁷ Se-selective HR-HMBC and ⁷⁷ Se satellites in 1D ¹³ C spectra and examine their conformations using the Newman projection scheme.

Hierarchical Structure and Molecular Dynamics of Metal-Organic Framework as Characterized by Solid State NMR

Metal-organic framework (MOF) stands out as a promising material with great potential in application areas, such as gas separation and catalysis, due to its extraordinary properties. In order to fully characterize the structure of MOFs, especially those without single crystal, Solid State NMR (SSNMR) is an indispensable tool. As a complimentary analytical technique to X-ray diffraction, SSNMR could provide detailed atomic level structure information. Meanwhile, SSNMR can characterize molecular dynamics over a wide dynamics range. In this review, selected applications of SSNMR on various MOFs are summarized and discussed.

The effect of nanoclay on the rheology and dynamics of polychlorinated biphenyl

The thermal, rheological, and mechanical and dielectric relaxation properties of exfoliated dispersions of montmorillonite clay in a molecular liquid, polychlorobiphenyl (PCB), were studied. The viscosity enhancement at low concentrations of clay (≤5%) exceeded by a factor of 50 the increase obtainable with conventional fillers. However, the effect of the nanoclay on the local dynamics, including the glass transition temperature, was quite small. All materials herein conformed to density-scaling of the reorientation relaxation time of the PCB for a common value of the scaling exponent. A new relaxation process was observed in the mixtures, associated with PCB molecules in proximity to the clay surface. This process has an anomalously high dielectric strength, suggesting a means to exploit nanoparticles to achieve large electrical energy absorption. This lower frequency dispersion has a weaker dependence on pressure and density, consistent with dynamics constrained by interactions with the particle surface.

Folding of Polymer Chains in the Early Stage of Crystallization

Understanding the structure formation of an ordered domain in the early stage of crystallization is one of the long-standing issues in polymer science. In this study, we investigate the chain trajectory of isotactic polypropylene (iPP) formed via rapid and deep quenching, using solid-state NMR spectroscopy. Comparisons of experimental and simulated ¹³C-¹³C double quantum (DQ) buildup curves demonstrated that individual iPP chains adopt adjacent re-entry sequences with an average folding number ⟨n⟩ = 3-4 in the mesomorphic form, assuming an adjacent re-entry fraction ⟨F⟩ of 100%. Therefore, long flexible polymer chains naturally fold in the early stage of crystallization, and folding-initiated nucleation results in formation of mesomorphic nanodomains.

Effect of PEO molecular weight on the miscibility and dynamics in epoxy/PEO blends

In this work, the effect of poly(ethylene oxide) (PEO) molecular weight in blends of epoxy (ER) and PEO on the miscibility, inter-chain weak interactions and local dynamics were systematically investigated by multi-frequency temperature modulation DSC and solid-state NMR techniques. We found that the molecular weight (M(w)) of PEO was a crucial factor in controlling the miscibility, chain dynamics and hydrogen bonding interactions between PEO and ER. A critical PEO molecular weight (M(crit)) around 4.5k was found. PEO was well miscible with ER when the molecular weight was below M(crit), where the chain motion of PEO was restricted due to strong inter-chain hydrogen bonding interactions. However, for the blends with high molecular weight PEO (M(w) > M(crit)), the miscibility between PEO and ER was poor, and most of PEO chains were considerably mobile. Finally, polarization inversion spin exchange at magic angle (PISEMA) solid-state NMR experiment further revealed the different mobility of the PEO in ER/PEO blends with different molecular weight of PEO at molecular level. Based on the DSC and NMR results, a tentative model was proposed to illustrate the miscibility in ER/PEO blends.

Unique molecular dynamics of structural elements in an asymmetric Janus bisamide supramolecule characterized by solid-state NMR

An asymmetric tapered Janus bisamide supramolecule consisting of 1,4-bis[3,4,5-tris(alkan-1-yloxy)benzamido]benzene bisamide (abbreviated as C22PhBAEO3) can possess three-dimensional (3D) long-range order under mild thermal treatment conditions. To understand its structural formation and unique phase-transition processes, the locally detailed structure and molecular dynamics of its structural elements in disordered and ordered phases of C22PhBAEO3 were investigated using various solid-state (SS) NMR techniques at the atomic level. On the basis of the determined conformations and packing structures of the alkyl chains in ordered and disordered crystalline phases, along with the geometry and kinetic parameters of the structural elements' dynamics, this study addresses the self-assembly, the phase-transition mechanisms, and the relationship between the structure and dynamics of these asymmetric Janus bisamide supramolecules.

Solid-state NMR in macromolecular systems: insights on how molecular entities move

The function of synthetic and natural macromolecularsystems critically depends on the packing and dynamics of the individual components of a given system. Not only can solid-state NMR provide structural information with atomic resolution, but it can also provide a way to characterize the amplitude and time scales of motions over broad ranges of length and time. These movements include molecular dynamics, rotational and translational motions of the building blocks, and also the motion of the functional species themselves, such as protons or ions. This Account examines solid-state NMR methods for correlating dynamics and function in a variety of chemical systems. In the early days, scientists thought that the rotationalmotions reflected the geometry of the moving entities. They described these phenomena as jumps about well-defined axes, such as phenyl flips, even in amorphous polymers. Later, they realized that conformational transitions in macromolecules happen in a much more complex way. Because the individual entities do not rotate around well-defined axes, they require much less space. Only recently researchers have appreciated the relative importance of large angle fluctuations of polymers over rotational jumps. Researchers have long considered that cooperative motions might be at work, yet only recently they have clearly detected these motions by NMR in macromolecular and supramolecular systems. In correlations of dynamics and function, local motions do not always provide the mechanism of long-range transport. This idea holds true in ion conduction but also applies to chain transport in polymer melts and semicrystalline polymers. Similar chain motions and ion transport likewise occur in functional biopolymers, systems where solid-state NMR studies are also performed. In polymer science, researchers have appreciated the unique information on molecular dynamics available from advanced solid-state NMR at times, where their colleagues in the biomacromolecular sciences have emphasized structure. By contrast, following X-ray crystallographers, researchers studying proteins using solution NMR introduced the combination of NMR with computer simulation before that became common practice in solid-state NMR. Today's simulation methods can handle partially ordered or even disordered systems common in synthetic polymers. Thus, the multitechnique approaches employed in NMR of synthetic and biological macromolecules have converged. Therefore, this Account will be relevant to both researchers studying synthetic macromolecular and supramolecular systems and those studying biological complexes.

Investigating the motion of diblock copolymer assemblies in ionic liquids by in situ electron microscopy

The movement of individual block copolymer micelles in free-standing films of ionic liquids is investigated by transmission electron microscopy with the aim of providing an easily accessible high-resolution imaging tool for the in situ observation of particle movement in a liquid environment. A proof of concept and first studies on the behavior of individual particles in the fluid are demonstrated.

Use of X-ray diffraction, molecular simulations, and spectroscopy to determine the molecular packing in a polymer-fullerene bimolecular crystal

The molecular packing in a polymer: fullerene bimolecular crystal is determined using X-ray diffraction (XRD), molecular mechanics (MM) and molecular dynamics (MD) simulations, 2D solid-state NMR spectroscopy, and IR absorption spectroscopy. The conformation of the electron-donating polymer is significantly disrupted by the incorporation of the electron-accepting fullerene molecules, which introduce twists and bends along the polymer backbone and 1D electron-conducting fullerene channels.

Reorientational Dynamics of Organophosphate Glass Formers – a Joint Study by 31P NMR, Dielectric Spectroscopy and Light Scattering

We study molecular reorientation in the glass formers triethyl-, tripropyl-, and m-tricresyl phosphate by measuring 31P NMR spectra, relaxation (T 1 and T 2), stimulated echo decays and two-dimensional spectra over a large temperature range (130–370 K). The results are compared to those from dielectric spectroscopy (DS) and depolarized light scattering (LS). While the time constants τ α of the primary (α-) process in the range  × 10−11–100 s well agree, the stretching of the reorientational correlation function is probe dependent, i.e., the rank-two functions (NMR and LS) essentially agree whereas the rank-one function (DS) is less stretched. The very similar 2D spectra recorded as a function of mixing time demonstrate that the reorientational mechanism does not significantly vary among the super-cooled liquids. A model of combining large- and small-angle reorientation allows for reproducing the 2D spectra and may be taken as generic for the dynamics in viscous molecular liquids. Pronounced secondary (β-) processes do not only effect the NMR relaxation but can be identified directly in the time domain by the stimulated echo technique. This becomes possible due to its broad time window (10 μs–100 s). Thus, applying the different 1D and 2D techniques makes 31P NMR well suited to probe molecular reorientation over a wide dynamic range.

Molecular Order and Dynamics of Tris(2-ethylhexyl)phosphate Confined in Uni-Directional Nanopores

Infrared Transition Moment Orientational Analysis (IR–TMOA) and Broadband Dielectric Spectroscopy (BDS) are combined to study molecular order and dynamics of the glass-forming liquid Tris(2-ethylhexy)phosphate (TEHP) confined in uni-directional nanopores with diameters of 4, 8, and 10.4 nm. The former method enables one to determine the molecular order parameter of specific IR transition moments. It is observed that the central P=O moiety of TEHP has a weak orientational effect (molecular order parameter S z = −0.1 ± 0.04) due the nanoporous confinement, in contrast to the terminal C–H groups. BDS traces the dynamic glass transition of the guest molecules in a broad spectral range and at widely varying temperature. An enhancement of the mobility takes place when approaching the glass transition temperature and becomes more pronounced with decreasing pore diameter. This is attributed to a slight reduction of the density of the confined liquid caused by the 2-dimensional geometrical constraint.

Equipping metallo-supramolecular macrocycles with functional groups: assemblies of pyridine-substituted urea ligands

A series of di-(m-pyridyl)-urea ligands were prepared and characterized with respect to their conformations by NOESY experiments and crystallography. Methyl substitution in different positions of the pyridine rings provides control over the position of the pyridine N atoms relative to the urea carbonyl group. The ligands were used to self-assemble metallo-supramolecular M(2)L(2) and M(3)L(3) macrocycles which are generated in a finely balanced equilibrium in DMSO and DMF according to DOSY NMR experiments and ESI FTICR mass spectrometry. Again, crystallography was used to characterize the assemblies. Methyl substitution in positions next to the pyridine nitrogen prevents coordination, while the other ligands form small metallo-supramolecular macrocycles. The incorporated urea carbonyl groups provide hydrogen bonding sites which converge towards the center of the assemblies.

Heterogeneous diffusion in thin polymer films as observed by high-temperature single-molecule fluorescence microscopy

Single-molecule fluorescence microscopy was used to investigate the dynamics of perylene diimide (PDI) molecules in thin supported polystyrene (PS) films at temperatures up to 135 °C. Such high temperatures, so far unreached in single-molecule spectroscopy studies, were achieved using a custom-built setup which allows for restricting the heated mass to a minimum. This enables temperature-dependent single-molecule fluorescence studies of structural dynamics in the temperature range most relevant to the processing and to applications of thermoplastic materials. In order to ensure that polymer chains were relaxed, a molecular weight of 3000 g/mol, clearly below the entanglement length of PS, was chosen. We found significant heterogeneities in the motion of single PDI probe molecules near T(g). An analysis of the track radius of the recorded single-probe molecule tracks allowed for a distinction between mobile and immobile molecules. Up to the glass transition temperature in bulk, T(g,bulk), probe molecules were immobile; at temperatures higher than T(g,bulk) + 40 K, all probe molecules were mobile. In the range between 0 and 40 K above T(g,bulk) the fraction of mobile probe molecules strongly depends on film thickness. In 30-nm thin films mobility is observed at lower temperatures than in thick films. The fractions of mobile probe molecules were compared and rationalized using Monte Carlo random walk simulations. Results of these simulations indicate that the observed heterogeneities can be explained by a model which assumes a T(g) profile and an increased probability of probe molecules remaining at the surface, both effects caused by a density profile with decreasing polymer density at the polymer-air interface.