Self-Assembly of DNA and RNA Building Blocks Explored by Nitrogen-14 NMR Crystallography: Structure and Dynamics

The isotopic enrichment of nucleic acids with nitrogen-15 is often carried out by solid-phase synthesis of oligonucleotides using phosphoramidite precursors that are synthetically demanding and expensive. These synthetic challenges, combined with the overlap of chemical shifts, explain the lag of nitrogen-15 NMR studies of nucleic acids behind those of proteins. For the structural characterization of DNA and RNA-related systems, new NMR methods that exploit the naturally occurring 99.9 % abundant nitrogen-14 isotope are therefore highly desirable. In this study, we have investigated nitrogen-14 spectra of self-assembled quartets based on the nucleobase guanine in the solid state by means of magic-angle spinning NMR spectroscopy. The network of dipolar proton–nitrogen couplings between neighboring stacked purine units is probed by 2D spectra based on ¹H→¹⁴N→¹H double cross-polarization. Interplane dipolar contacts are identified between the stacked G quartets. The assignment is supported by density functional theory (DFT) calculations of the anisotropic chemical shifts and quadrupolar parameters. The experimental spectra are fully consistent with internuclear distances obtained in silico. Averaging of chemical shifts due to internal motions can be interpreted by semiempirical calculations. This method can easily be extended to synthetic G quartets based on nucleobase or nucleoside analogs and potentially to oligonucleotides.     

Cross-Polarisation Applied to the Study of Liquid Crsytalline Ordering

 Cross polarisation is extensively used in solid state NMR for enhancing signals of nuclei with low gyromagnetic ratio. However, the use of the method for providing quantitative structural and dynamics information is limited. This arises due to the fact that the mechanism which is responsible for cross polarisation namely, the dipolar interaction, has a long range and is also anisotropic. In nematic liquid crystals these limitations are easily overcome since molecules orient in a magnetic field. The uniaxial ordering of the molecules essentially removes problems associated with the angular dependence of the interactions encountered in powdered solids. The molecular motion averages out intermolecular dipolar interaction, while retaining partially averaged intramolecular interaction. In this article the use of cross polarisation for obtaining heteronuclear dipolar couplings and hence the order parameters of liquid crystals is presented. Several modifications to the basic experiment were considered and their utility illustrated. A method for obtaining proton–proton dipolar couplings, by utilizing cross polarisation from the dipolar reservoir, is also presented.     

Nuclear magnetic resonance of rapidly rotated elastomers

The NMR line narrowing effect by high speed rotation of the specimen at the magic angle is observed in several elastomers at room temperature. The ¹H and ¹⁹F chemical shifts thus revealed permit the investigation of the monomer ratio and conformational structure in copolymers. Using a weak collision relaxation model, we explain the possibility of line narrowing in elastomers by the existence of slow inter-chain motion; the observed limiting line-width is attributed to rapid segmental motion. Our experiences allow us to determine these two correlation times for elastomers under investigation. This procedure is also applied to viscous polymer solutions.     

Molecular dynamics in paramagnetic materials as studied by magic-angle spinning 2H NMR spectra

A magic-angle spinning (MAS) 2H NMR experiment was applied to study the molecular motion in paramagnetic compounds. The temperature dependences of 2H MAS NMR spectra were measured for paramagnetic [M(H2O)6][SiF6] (M=Ni2+, Mn2+, Co2+) and diamagnetic [Zn(H2O)6][SiF6]. The paramagnetic compounds exhibited an asymmetric line shape in 2H MAS NMR spectra because of the electron-nuclear dipolar coupling. The drastic changes in the shape of spinning sideband patterns and in the line width of spinning sidebands due to the 180 degrees flip of water molecules and the reorientation of [M(H2O)6]2+ about its C3 axis were observed. In the paramagnetic compounds, paramagnetic spin-spin relaxation and anisotropic g-factor result in additional linebroadening of each of the spinning sidebands. The spectral simulation of MAS 2H NMR, including the effects of paramagnetic shift and anisotropic spin-spin relaxation due to electron-nuclear dipolar coupling and anisotropic g-factor, was performed for several molecular motions. Information about molecular motions in the dynamic range of 10(2) s(-1)相似文献   

Cross-Polarisation Applied to the Study of Liquid Crsytalline Ordering

Summary.  Cross polarisation is extensively used in solid state NMR for enhancing signals of nuclei with low gyromagnetic ratio. However, the use of the method for providing quantitative structural and dynamics information is limited. This arises due to the fact that the mechanism which is responsible for cross polarisation namely, the dipolar interaction, has a long range and is also anisotropic. In nematic liquid crystals these limitations are easily overcome since molecules orient in a magnetic field. The uniaxial ordering of the molecules essentially removes problems associated with the angular dependence of the interactions encountered in powdered solids. The molecular motion averages out intermolecular dipolar interaction, while retaining partially averaged intramolecular interaction. In this article the use of cross polarisation for obtaining heteronuclear dipolar couplings and hence the order parameters of liquid crystals is presented. Several modifications to the basic experiment were considered and their utility illustrated. A method for obtaining proton–proton dipolar couplings, by utilizing cross polarisation from the dipolar reservoir, is also presented. Corresponding author. E-mail: kvr@sif.iisc.ernet.in Received May 28, 2002; accepted June 19, 2002     

Characterization of H2-Splitting Products of Frustrated Lewis Pairs: Benefit of Fast Magic-Angle Spinning

Proton spectroscopy in solid-state NMR on catalytic materials offers new opportunities in structural characterization, in particular of reaction products of catalytic reactions such as hydrogenation reactions. Unfortunately, the ¹H NMR line widths in magic-angle spinning solid-state spectra are often broadened by an incomplete averaging of ¹H-¹H dipolar couplings. We herein discuss two model compounds, namely the H₂-splitting products of two phosphane-borane Frustrated Lewis Pairs (FLPs), to study potentials and limitations of proton solid-state NMR experiments employing magic-angle spinning frequencies larger than 100 kHz at a static magnetic field strength of 20.0 T. The ¹H lines are homogeneously broadened as illustrated by spin-echo decay experiments. We study two structurally similar materials which however show significant differences in ¹H line widths which we explain by differences in their ¹H-¹H dipolar networks. We discuss the benefit of fast MAS experiments up to 110 kHz to detect the resonances of the H⁺/H⁻ pair in the hydrogenation products of FLPs.     

1H‐19F REDOR‐filtered NMR spin diffusion measurements of domain size in heterogeneous polymers

Solid state NMR spectroscopy is inherently sensitive to chemical structure and composition and thus makes an ideal method to probe the heterogeneity of multicomponent polymers. Specifically, NMR spin diffusion experiments can be used to extract reliable information about spatial domain sizes on multiple length scales, provided that magnetization selection of one domain can be achieved. In this paper, we demonstrate the preferential filtering of protons in fluorinated domains during NMR spin diffusion experiments using ¹H‐¹⁹F heteronuclear dipolar dephasing based on rotational echo double resonance (REDOR) MAS NMR techniques. Three pulse sequence variations are demonstrated based on the different nuclei detected: direct ¹H detection, plus both ¹H?¹³C cross polarization and ¹H?¹⁹F cross polarization detection schemes. This ¹H‐¹⁹F REDOR‐filtered spin diffusion method was used to measure fluorinated domain sizes for a complex polymer blend. The efficacy of the REDOR‐based spin filter does not rely on spin relaxation behavior or chemical shift differences and thus is applicable for performing NMR spin diffusion experiments in samples where traditional magnetization filters may prove unsuccessful. This REDOR‐filtered NMR spin diffusion method can also be extended to other samples where a heteronuclear spin pair exists that is unique to the domain of interest.     

Measurement of Large Dipolar Couplings of a Liquid Crystal with Terminal Phenyl Rings and Estimation of the Order Parameters

NMR spectroscopy is a powerful means of studying liquid‐crystalline systems at atomic resolutions. Of the many parameters that can provide information on the dynamics and order of the systems, ¹H–¹³C dipolar couplings are an important means of obtaining such information. Depending on the details of the molecular structure and the magnitude of the order parameters, the dipolar couplings can vary over a wide range of values. Thus the method employed to estimate the dipolar couplings should be capable of estimating both large and small dipolar couplings at the same time. For this purpose, we consider here a two‐dimensional NMR experiment that works similar to the insensitive nuclei enhanced by polarization transfer (INEPT) experiment in solution. With the incorporation of a modification proposed earlier for experiments with low radio frequency power, the scheme is observed to enable a wide range of dipolar couplings to be estimated at the same time. We utilized this approach to obtain dipolar couplings in a liquid crystal with phenyl rings attached to either end of the molecule, and estimated its local order parameters.     

Broad-line NMR studies of molecular motion in cured epoxy resins

The conformation of network chain segments in a rigid glassy DDM-cured bisphenol A epoxy resin has been determined by means of rotational isomeric-state model and confirmed by conformity of experimental NMR second moments with a theoretical estimate based on the model. The glass transition temperatures T_g have been determined from precipitate NMR line narrowing with increase in temperature due to the onset of rapid (>10⁴ Hz) main-chain molecular motion. The temperature dependence of the correlation frequency has been determined and the type and extent of molecular motion that occurs in such epoxy resins is discussed.     

Colossal Anisotropic Thermal Expansion in a Diazo-Functionalized Compound with Switchable Solid-State Behavior

Achieving substantial anisotropic thermal expansion (TE) in solid-state materials is challenging as most materials undergo volumetric expansion upon heating. Here, we describe colossal, anisotropic TE in crystals of an organic compound functionalized with two azo groups. Interestingly, the material exhibits distinct and switchable TE behaviors within different temperature regions. At high temperature, two-dimensional, area zero TE and colossal, positive linear TE (α=211 MK⁻¹) are attained due to dynamic motion, while at low temperature, moderate positive TE occurs in all directions. Investigation of the solid-state motion showed the change in enthalpy and entropy are quite different in the two temperature regions and solid-state NMR experiments support motion in the solid. Cycling experiments demonstrate that the solid-state motions and TE behaviors are completely reversible. These results reveal strategies for designing significant anisotropic and switchable behaviors in solid-state materials.     

Systematic Dielectric and NMR Study of the Ionic Liquid 1‐Alkyl‐3‐Methyl Imidazolium

The dynamic behaviors of ionic liquid samples consisting of a series of 1‐alkyl‐3‐methylimidazolium cations and various counteranionic species are investigated systematically over a wide frequency range from 1 MHz to 20 GHz at room temperature using dielectric relaxation (DR) and nuclear magnetic resonance (NMR) spectroscopies. DR spectra for the ionic liquids are reasonably deconvoluted into two or three relaxation modes. The slowest relaxation times are strongly dependent upon sample viscosity and cation size, whereas the relaxation times of other modes are almost independent of these factors. We attribute the two slower relaxation modes to the rotational relaxation modes of the dipolar cations because the correlation times of the cations evaluated using longitudinal relaxation time (T₁ ¹³C NMR) measurements corresponded to the dielectric relaxation times. On the other hand, the fastest relaxation mode is presumably related to the inter‐ion motions of ion‐pairs formed between cationic and anionic species. In the case of the ionic liquid bis(trifluoromethanesulfonyl)imide, the system shows marked dielectric relaxation behavior due to rotational motion of dipolar anionic species in addition to the relaxation modes attributed to the dipolar cations.     

Real-Time Monitoring Polymerization Reactions Using Dipolar Echoes in 1H Time Domain NMR at a Low Magnetic Field

¹H time domain nuclear magnetic resonance (¹H TD-NMR) at a low magnetic field becomes a powerful technique for the structure and dynamics characterization of soft organic materials. This relies mostly on the method sensitivity to the ¹H-¹H magnetic dipolar couplings, which depend on the molecular orientation with respect to the applied magnetic field. On the other hand, the good sensitivity of the ¹H detection makes it possible to monitor real time processes that modify the dipolar coupling as a result of changes in the molecular mobility. In this regard, the so-called dipolar echoes technique can increase the sensitivity and accuracy of the real-time monitoring. In this article we evaluate the performance of commonly used ¹H TD-NMR dipolar echo methods for probing polymerization reactions. As a proof of principle, we monitor the cure of a commercial epoxy resin, using techniques such as mixed-Magic Sandwich Echo (MSE), Rhim Kessemeier—Radiofrequency Optimized Solid Echo (RK-ROSE) and Dipolar Filtered Magic Sandwich Echo (DF-MSE). Applying a reaction kinetic model that supposes simultaneous autocatalytic and noncatalytic reaction pathways, we show the analysis to obtain the rate and activation energy for the epoxy curing reaction using the NMR data. The results obtained using the different NMR methods are in good agreement among them and also results reported in the literature for similar samples. This demonstrates that any of these dipolar echo pulse sequences can be efficiently used for monitoring and characterizing this type of reaction. Nonetheless, the DF-MSE method showed intrinsic advantages, such as easier data handling and processing, and seems to be the method of choice for monitoring this type of reaction. In general, the procedure is suitable for characterizing reactions involving the formation of solid products from liquid reagents, with some adaptations concerning the reaction model.     

Polyacetylenes as enantiodifferentiating alignment media

Orientation help: Valine-derived polyacetylenes are introduced as enantiomer-differentiating alignment media. The F2-coupled HSQC-type NMR spectra of both enantiomers of isopinocampheol (IPC) display narrow line widths allowing for the precise extraction of residual dipolar couplings (black contour plot: (+)-IPC in an isotropic phase, blue: (-)-IPC in an anisotropic phase, and red: (+)-IPC in an anisotropic phase; J=coupling constant).     

Study of the residual dipolar coupling by 1H NMR MAS technique. Effect of the grafting ratio on interface polymer grafted on silica

¹H NMR permits some approaches to a monomer unit scale of the macromolecular grafted on the solid. In the case of poly(ethylene) grafted on silica, the magic angle spinning technique confirms, by narrowing of the central line and apparition of side bands, the existence of the residual dipolar interaction, which reveals the high monomer unit concentration at the surface. The study of the side bands permits calculation of the physical parameter: the second moment, which gives in turn an indication of the evolution of the monomer unit concentration on the surface. This behavior has been studied as a function of molecular weight of the chains and grafting ratio. A fair agreement is obtained for the second moment and the linewidth, giving a consistent picture by two independent techniques: magnetic relaxation and magic angle spinning.     

A dipolar coupling based strategy for simultaneous resonance assignment and structure determination of protein backbones.

A new approach for simultaneous protein backbone resonance assignment and structure determination by NMR is introduced. This approach relies on recent advances in high-resolution NMR spectroscopy that allow observation of anisotropic interactions, such as dipolar couplings, from proteins partially aligned in field ordered media. Residual dipolar couplings are used for both geometric information and a filter in the assembly of residues in a sequential manner. Experimental data were collected in less than one week on a small redox protein, rubredoxin, that was 15N enriched but not enriched above 1% natural abundance in 13C. Given the acceleration possible with partial 13C enrichment, the protocol described should provide a very rapid route to protein structure determination. This is critical for the structural genomics initiative where protein expression and structural determination in a high-throughput manner will be needed.     

The dynamics of the CH3CN molecule in the isotropic phase and in a nematic solution

Abstract

NMR lineshape studies of acelonitrile in the isotropic and the liquid-crystalline nematic phase of PCH have been performed. The scalar relaxation of the second kind due to the presence of the ¹⁴N quadrupolar nucleus has been confirmed as the most important relaxation mechanism for this molecule in both the isotropic and the anisotropic phase. It has been found largely responsible for the selective broadening on ¹³C and ¹H transitions. A minor contribution arising from intramolecular dipolar relaxation mechanism has also been investigated. Linewidth analysis of the NMR spectra allowed us to determine the quadrupolar relaxation time T _IN of the ¹⁴N nucleus. This is connected to the correlation time for rotational diffusion perpendicular to the molecular symmetry axis. A possible explanation of a residual selective broadeining which effects the ¹³C and ¹H NMR transitions and is not taken into account by this mechanism, is also given.     

H NMR studies of poly(N-isopropylacrylamide) gels near the phase transition

The phase transition and critical phenomenon of equilibrium swollen poly(N-isopropylacrylamide) (NIPA) hydrogels were studied by ¹H NMR spectroscopy in liquid solution mode. The quantitative NMR observation shows that the peak height and line width of polymer proton and of the HOD proton, and relaxation times of HOD proton all transitionally change as the temperature approaches the transition temperature. The relaxation times of water protons are also measured quantitatively, which shows that the temperature dependence of relaxation times of HOD on temperature before the transition is not consistent with relaxation theory based on the assumption of dominated dipolar interaction between like-spin nuclei and isotropic rotational motion. To explain the surprising relaxation behavior of HOD, we suggest that the amount of bound water in gels increases gradually with temperature at the approach of the phase transition. The pulsed-gradient spin-echo NMR experiments of NIPA gel confirm this suggestion. We believe that these results have important implications concerning the mechanism of the phase transition of NIPA hydrogels.     

2H NMR characterization of phenylene ring flip motion in poly(p-phenylene vinylene) films

Solid-state ²H quadrupole echo nuclear magnetic resonance (NMR) spectra and measurements of ²H spin lattice relaxation times have been obtained for films of poly(p-phenylene vinylene) deuterated in phenylene ring positions (PPV-d₄). NMR line shapes show that all the phenylene rings of PPV undergo 180° rotational jumps about the 1,4 ring axis (“ring flips”) at 225°C. The temperature dependence of the ²H line shapes show that the jump motion is thermally activated, with a median activation energy, E_a = 15 kcal/mol, and a distribution of activation energies of less than ±2 kcal/mol. The jump rate was also determined from the magnitude of the anisotropic T₂ relaxation associated with ²H line shapes and from the curvature of inversion recovery intensity data. The experimental activation energy for jumps is comparable to the intramolecular potential barrier for rotation about phenylene vinylene bonds. ²H NMR provides a method for determining the phenylene-vinylene rotational barrier in pristine PPV, and may potentially be used to study conjugation in conducting films.