Segmental versus chain dynamics of linear polymers

Segmental dynamics of relatively short linear polymers are discussed in terms of two distinct contributions, one related to the local segmental motion (alpha relaxation) and the other to polymer-specific effects that reflect Brownian dynamics of the polymer under chain connectivity constraints (Rouse relaxation modes). These two aspects of polymer dynamics are reflected, though differently, in relaxation spectra of different experimental techniques. Two contrasting cases of the (collective) dipolar response (dielectric techniques) versus the individual segmental response (e.g., NMR spin-lattice relaxation spectroscopy) are considered. The second-rank orientational correlation function of an elementary (Kuhn) segment, directly related to NMR observables, is derived in terms of Rouse normal modes. The effect of alpha dynamics is estimated under the assumption of a separation of time scales which, as it is argued, is a necessary precondition of the Rouse approach. The relative magnitude of the polymer-related dynamics is expressed through the number of elementary Rouse units in the chain and the number of Kuhn segments in a Rouse unit. The results are discussed in the context of recent literature.     

The study of structure and dynamics of molecules: NMR spectra transformed by superfine coupling

In the present paper, the peculiarities of NMR phenomenon in paramagnetic systems are reported. Specifics of detection of high‐resolution NMR spectra transformed by superfine interaction are discussed. Concrete examples illustrate the modern possibilities of NMR application for the study of structure and dynamics of the molecular (multielectron) systems. Copyright © 2015 John Wiley & Sons, Ltd.     

Nuclear magnetic resonance and dielectric noise study of spectral densities and correlation functions in the glass forming monoalcohol 2-ethyl-1-hexanol

The spectral densities related to various relaxation processes of the glass former 2-ethyl-1-hexanol (2E1H), a monohydroxy alcohol, are probed using several nuclear magnetic resonance (NMR) experiments as well as via dielectric noise spectroscopy (DNS). On the basis of the spectral density relating to voltage fluctuations, i.e., without the application of external electrical fields, DNS enables the detection of the structural relaxation and of the prominent, about two decades slower Debye process. The NMR-detected spectral density, sensitive to the orientational fluctuations of the hydroxyl deuteron, also reveals dynamics slower than the structural relaxation, but not as slow as the Debye process. Rotational and translational correlation functions of 2E1H are probed using stimulated-echo NMR techniques which could only resolve the structural dynamics or faster processes. The experimental results are discussed with reference to models that were suggested to describe the dynamics in supercooled alcohols.     

Motional heterogeneity of intercalated species in modified clays and poly(epsilon-caprolactone)/clay nanocomposites

Modified laponites and synthetic saponites are used as precursors for the preparation of poly(epsilon-caprolactone) (PCL)/clay nanocomposites. The structure and dynamics of species intercalated in the modified clays and the corresponding nanocomposites are characterized by X-ray diffraction and magic-angle spinning NMR. The influence of the headgroup, the hydrocarbon chain length, and the loading of the surfactant on the nanocomposite formation are discussed. The yield of PCL intercalation is related to the probability of direct polymer-clay interactions and to the size of the clay platelets. Relaxation times in the laboratory and rotating frames that allow characterization of fast and slow molecular dynamics in these systems are discussed, showing a motional heterogeneity of the intercalated species.     

Mechanisms and Beyond: Elucidation of Fluxional Dynamics by Exchange NMR Spectroscopy

Detailed mechanistic information is crucial to our understanding of reaction pathways and selectivity. Dynamic exchange NMR techniques, in particular 2D exchange spectroscopy (EXSY) and its modifications, provide indispensable intricate information on the mechanisms of organic and inorganic reactions and other phenomena, for example, the dynamics of interfacial processes. In this Review, key results from exchange NMR studies of small molecules over the last few decades are systemised and discussed. After a brief introduction to the theory, the key types of dynamic processes are identified and fundamental examples given of intra- and intermolecular reactions, which, in turn, could involve, or not, bond-making and bond-breaking events. Following that logic, internal molecular rotation, intramolecular stereomutation and molecular recognition will first be considered because they do not typically involve bond breaking. Then, rearrangements, substitution-type reactions, cyclisations, additions and other processes affecting chemical bonds will be discussed. Finally, interfacial molecular dynamics and unexpected combinations of different types of fluxional processes will also be highlighted. How exchange NMR spectroscopy helps to identify conformational changes, coordination and molecular recognition processes as well as quantify reaction energy barriers and extract detailed mechanistic information by using reaction rate theory in conjunction with computational techniques will be shown.     

NMR of membrane-associated peptides and proteins

In living cells, membrane proteins are essential to signal transduction, nutrient use, and energy exchange between the cell and environment. Due to challenges in protein expression, purification and crystallization, deposition of membrane protein structures in the Protein Data Bank lags far behind existing structures for soluble proteins. This review describes recent advances in solution NMR allowing the study of a select set of peripheral and integral membrane proteins. Surface-binding proteins discussed include amphitropic proteins, antimicrobial and anticancer peptides, the HIV-1 gp41 peptides, human alpha-synuclein and apolipoproteins. Also discussed are transmembrane proteins including bacterial outer membrane beta-barrel proteins and oligomeric alpha-helical proteins. These structural studies are possible due to solubilization of the proteins in membrane-mimetic constructs such as detergent micelles and bicelles. In addition to protein dynamics, protein-lipid interactions such as those between arginines and phosphatidylglycerols have been detected directly by NMR. These examples illustrate the unique role solution NMR spectroscopy plays in structural biology of membrane proteins.     

Molecular and supramolecular dynamics of hybrid organic-inorganic interfaces for the rational construction of advanced hybrid nanomaterials

Today the capability to rationally design and construct hybrid materials utilizing a performance-property driven methodology is strongly dependent on our ability to control the structure and the dynamics of hybrid interfaces. This control needs a deep knowledge of their molecular and supramolecular dynamics that must be evaluated in situ, in the soft matter or colloidal states. For this purpose the use of modern methodologies of characterization such as time resolved synchrotron experiments and advanced pulsed field gradient NMR methods (DOSY) is particularly relevant. In this critical review, two important examples are discussed. They concern, first, the study of surface capping organic components' affinity towards nanoparticle surfaces by DOSY NMR. The knowledge and therefore the tuning of this affinity is paramount because it controls solubility, transferability and stability of colloidal dispersions of nanoparticles (NPs). In the second part, the mechanism of micellar templated formation of hybrid mesophases will be discussed in the frame of the main results obtained via in situ SAXS (107 references).     

On the orientational dependence of resolution in 1H solid-state NMR, and its role in MAS, CRAMPS and delayed-acquisition experiments

Numerical simulations and experiments are used to show that the spin dynamics of the dipolar-coupled networks in solids is often strongly dependent on crystallite orientation. In particular, different rates of dephasing of the magnetisation mean that NMR signals obtained at longer dephasing times are dominated by orientations in which the local dipolar coupling strength is relatively weak. This often leads to a distinct improvement in spectral resolution as the dephasing time is increased. The effects are particularly noticeable under magic-angle spinning (MAS), but are also observed when homonuclear decoupling is used to reduce the rate of dipolar dephasing. Numerical simulation is seen to be a powerful and easily used tool for understanding the behaviour of solid-state NMR experiments involving dipolar-coupled networks. The implications for solid-state NMR spectra of abundant spins acquired under MAS and homonuclear decoupling are discussed, as well as insights provided into the performance of 'delayed-acquisition' and 'constant-time' experiments.     

Dynamics and conformations of PEO chains chemically bonded on silica: comparison between 1H and 2H NMR

1H NMR was used to study the motion of monomer units in a layer of poly(ethylene oxide) chains grafted on silica. First, the dependence of the relaxation times on the grafting ratios is discussed qualitatively from a phenomenological point of view. Next, the NMR line narrowing effect by high-speed rotation is observed in the same samples with different grafting ratios. The magic angle spinning technique permits determination of two correlation times for each grafting ratio: tau(c) characteristic of an environment with a fast motion and tau(l) characteristic of an environment with a slow motion. In addition, the dynamics of these grafted chains are investigated by deuterium NMR (2H NMR), which is sensitive to the anisotropy of molecular motion. The evolution has been studied for two extreme grafting ratios and each time as a function of temperature. The anisotropy is more marked at low temperatures and for a low grafting ratio. The results are consistent with the 1H NMR relaxation times measured as a function of temperature.     

NMR and protein dynamics

NMR techniques can give insight into a wide variety of motional events that occur in proteins over a range of timescales. In the first section of this article an overview of the results of dynamics studies, using NMR methods, on both small globular and larger multi-domain proteins is presented including the findings from investigations of non-native partly folded states. The second section of the article then concentrates on two topics where NMR can give residue specific quantitative data, namely coupling constant measurements and relaxation studies, including comparisons of these NMR data with results from crystallographic studies and theoretical molecular dynamics simulations. Finally the possible functional significance of the experimentally observed motions in proteins is discussed. © 1996 John Wiley & Sons, Inc.     

Structure-function relationship of amino acid-[2]rotaxanes

Synthetic methodology was developed to construct amino acid-[2]rotaxanes that have phenylalanine and 3,5-di-tert-butylbenzene as blocking groups and dibenzo-24-crown-8, derivatized with either N-acetylargininyl or a carboxylic group, as the ring. A relative measure of the intramolecular interaction energies between the functional groups in DMSO/water mixtures is obtained by comparing their pK(a) values. Rotaxane structures were investigated through 2D NMR analysis and molecular dynamics simulations. Association constants for complexes of amino acids and rotaxanes in various protonation states were determined in a variety of solvent systems by (1)H NMR analysis. The unique intracomponent interactions that exist in the rotaxanes and their ability to act as artificial receptors are discussed.     

Dynamics and structure of a flexible columnar liquid crystal based on tetrabenzocyclododecatetraene

The dynamical and conformational behaviour of a flexible tetrabenzocyclododecatetraene derivative exhibiting a columnar mesophase has been studied by a combination of deuteron solid state NMR spectroscopy and molecular dynamics (MD) simulations. As shown by two-dimensional (2D) exchange NMR, the mesophase is characterized by slow axial reorientations (∼10^-3s) of single molecular units where the phenylene rings exhibit a well-defined quasi-fourfold potential, while the 2D spectra of the core methylene sites are sensitive to the molecular conformation and reorientation mechanism. Motional narrowing of one-dimensional (1D) spectra reveals additional fast librations due to the internal flexibility of the mesogenic moiety. The various reorientation pathways comprising interconversions and pseudo-rotations between different energetically stable conformations are elucidated on a microscopic level by molecular dynamics simulations. The mesophase dynamics is ascribed to a complex axial motion involving rotational jumps combined with a pseudo-rotation between two symmetry related sofa forms. This is confirmed quantitatively by comparing the experimental 2D NMR spectra of the core methylene sites and the simulations which are based on the molecular geometries obtained by MD simulations. The lineshapes of one- and two-dimensional spectra of magnetically aligned samples specific to the orientation behaviour of the sofa conformer are discussed.     

Towards Accurate Predictions of Proton NMR Spectroscopic Parameters in Molecular Solids

The factors contributing to the accuracy of quantum-chemical calculations for the prediction of proton NMR chemical shifts in molecular solids are systematically investigated. Proton chemical shifts of six solid amino acids with hydrogen atoms in various bonding environments (CH, CH₂, CH₃, OH, SH and NH₃) were determined experimentally using ultra-fast magic-angle spinning and proton-detected 2D NMR experiments. The standard DFT method commonly used for the calculations of NMR parameters of solids is shown to provide chemical shifts that deviate from experiment by up to 1.5 ppm. The effects of the computational level (hybrid DFT functional, coupled-cluster calculation, inclusion of relativistic spin-orbit coupling) are thoroughly discussed. The effect of molecular dynamics and nuclear quantum effects are investigated using path-integral molecular dynamics (PIMD) simulations. It is demonstrated that the accuracy of the calculated proton chemical shifts is significantly better when these effects are included in the calculations.     

Flexible self-assembling porphyrin supramolecules

The design and chemical synthesis of a series of hybrid flexible self-assembling supramolecules utilising both crown ether-naphthalene diimide host-guest chemistry and metalloporphyrin-pyridyl coordination is discussed. The resulting compound structures and dynamics are probed using a variety of techniques, including diffusion ordered NMR spectroscopy (DOSY) and cold-spray ionisation mass spectrometry (CSI-MS).     

Localized and Collective Motions in HET‐s(218‐289) Fibrils from Combined NMR Relaxation and MD Simulation

Nuclear magnetic resonance (NMR) relaxation data and molecular dynamics (MD) simulations are combined to characterize the dynamics of the fungal prion HET‐s(218‐289) in its amyloid form. NMR data is analyzed with the dynamics detector method, which yields timescale‐specific information. An analogous analysis is performed on MD trajectories. Because specific MD predictions can be verified as agreeing with the NMR data, MD was used for further interpretation of NMR results: for the different timescales, cross‐correlation coefficients were derived to quantify the correlation of the motion between different residues. Short timescales are the result of very local motions, while longer timescales are found for longer‐range correlated motion. Similar trends on ns‐ and μs‐timescales suggest that μs motion in fibrils is the result of motion correlated over many fibril layers.     

Complex Formation of the Tetracycline‐Binding Aptamer Investigated by Specific Cross‐Relaxation under DNP

While dynamic nuclear polarization (DNP) under magic‐angle spinning (MAS) is generally a powerful method capable of greatly enhancing the sensitivity of solid‐state NMR spectroscopy, hyperpolarization also gives rise to peculiar spin dynamics. Here, we elucidate how specific cross‐relaxation enhancement by active motions under DNP (SCREAM‐DNP) can be utilized to selectively obtain MAS‐NMR spectra of an RNA aptamer in a tightly bound complex with a methyl‐bearing ligand (tetracycline) due to the effective CH₃‐reorientation at an optimized sample temperature of approximately 160 K. SCREAM‐DNP can spectrally isolate the complex from non‐bound species in an RNA mixture. This selectivity allows for a competition assay between the aptamer and a mutant with compromised binding affinity. Variations in molecular structure and methyl dynamics, as observed by SCREAM‐DNP, between free tetracycline and RNA‐bound tetracycline are discussed.     

Efficient analysis of highly complex nuclear magnetic resonance spectra of flexible solutes in ordered liquids by using molecular dynamics

The NMR spectra of n-pentane as solute in the liquid crystal 5CB are measured at several temperatures in the nematic phase. Atomistic molecular dynamics simulations of this system are carried out to predict the dipolar couplings of the orientationally ordered pentane, and the spectra predicted from these simulations are compared with the NMR experimental ones. The simulation predictions provide an excellent starting point for analysis of the experimental NMR spectra using the covariance matrix adaptation evolutionary strategy. This shows both the power of atomistic simulations for aiding spectral analysis and the success of atomistic molecular dynamics in modeling these anisotropic systems.     

Rotor modulations and recoupling strategies in 13C solid-state magic-angle-spinning NMR spectroscopy: probing molecular orientation and dynamics.

Recoupling strategies for anisotropic interactions enable the investigation of molecular structure, order and dynamics in a sensitive and site-specific fashion by solid-state NMR spectroscopy. Whereas magic-angle spinning (MAS) efficiently averages anisotropic interactions and enhances spectral resolution, recoupling pulse sequences selectively restore certain parts of rotor-modulated dipole-dipole couplings or chemical shift anisotropies (CSA). More specifically, it is possible to recouple either the omegaR- or the 2omegaR-modulated terms of an interaction Hamiltonian, which exhibit different orientation dependencies and, in this way, provide a means of distinguishing whether the observed NMR spectra are affected by molecular motion or by molecular orientation. Sideband patterns generated by reconversion rotor encoding allow for a precise and selective determination of coupling constants and anisotropies, which contain site-specific information on structure, orientation and/or dynamics of individual molecular segments. Corresponding recoupling schemes are presented in a common context, and the possibilities of exploiting these effects for the determination of order parameters of oriented materials, such as oriented polymer chains or extruded fibres of a discotic mesogen, are discussed. The obtained orientational order parameters are compared to results from two-dimensional wide angle X-ray scattering (WAXS).     

Synthetic metallomolecules as agents for the control of DNA structure

This tutorial review summarises B-DNA structure and metallomolecule binding modes and illustrates some DNA structures induced by molecules containing metallic cations. The effects of aquated metal ions, cobalt amines, ruthenium octahedral metal complexes, metallohelicates and platinum complexes such as cis-platin are discussed alongside the techniques of NMR, X-ray crystallography, gel electrophoresis, circular dichroism, linear dichroism and molecular dynamics. The review will be of interest to people interested in both DNA structure and roles of metallomolecules in biological systems.     

Intermediate motions as studied by solid-state separated local field NMR experiments

In this report, the application of a class of separated local field NMR experiments named dipolar chemical shift correlation (DIPSHIFT) for probing motions in the intermediate regime is discussed. Simple analytical procedures based on the Anderson-Weiss (AW) approximation are presented. In order to establish limits of validity of the AW based formulas, a comparison with spin dynamics simulations based on the solution of the stochastic Liouville-von-Neumann equation is presented. It is shown that at short evolution times (less than 30% of the rotor period), the AW based formulas are suitable for fitting the DIPSHIFT curves and extracting kinetic parameters even in the case of jumplike motions. However, full spin dynamics simulations provide a more reliable treatment and extend the frequency range of the molecular motions accessible by DIPSHIFT experiments. As an experimental test, molecular jumps of imidazol methyl sulfonate and trimethylsulfoxonium iodide, as well as the side-chain motions in the photoluminescent polymer poly[2-methoxy-5-(2'-ethylhexyloxy)-1,4-phenylenevinylene], were characterized. Possible extensions are also discussed.