Exchange NMR Spectroscopy Research Articles

Kinetics of RNA Refolding in Dynamic Equilibrium by 1H-Detected 15N Exchange NMR Spectroscopy

By implementing new NMR methods that were designed to map very slow exchange processes we have investigated and characterized the refolding kinetics of a thermodynamically stable 34mer RNA sequence in dynamic equilibrium. The RNA sequence was designed to undergo a topologically favored conformational exchange between different hairpin folds, serving as a model to estimate the minimal time required for more complex RNA folding processes. Chemically prepared RNA sequences with sequence-selective (15)N labels provided the required signal separation and allowed a straightforward signal assignment of the imino protons by HNN correlation experiments. The 2D version of the new (1)H-detected (15)N exchange spectroscopy (EXSY) pulse sequence provided cross-peaks for resonances belonging to different folds that interchange on the time scale of longitudinal relaxation of (15)N nuclei bound to imino protons. The 34mer RNA sequence exhibits two folds which exchange on the observable time scale (tau(obs) approximately T(1){(15)Nu} < 5 s) and a third fold which is static on this time scale. A 1D version of the (15)N exchange experiment allowed the measurement of the exchange rates between the two exchanging folds as a function of temperature and the determination of the corresponding activation energies E(a) and frequency factors A. We found that the refolding rates are strongly affected by an entropically favorable preorientation of the replacing strand. The activation energies are comparable to values obtained for the slow refolding of RNA sequences of similar thermodynamic stability but less favorable topology.

7Li NMR and Two-Dimensional Exchange Study of Lithium Dynamics in Monoclinic Li3V2(PO4)3

High-resolution solid-state (7)Li NMR was used to characterize the structure and dynamics of lithium ion transport in monoclinic Li(3)V(2)(PO(4))(3). Under fast magic-angle spinning (MAS) conditions (25 kHz), three resonances are clearly resolved and assigned to the three unique crystallographic sites. This assignment is based on the Fermi-contact delocalization interaction between the unpaired d-electrons at the vanadium centers and the lithium ions. One-dimensional variable-temperature NMR and two-dimensional exchange spectroscopy (EXSY) are used to probe Li mobility between the three sites. Very fast exchange, on the microsecond time scale, was observed for the Li hopping processes. Activation energies are determined and correlated to structural properties including interatomic Li distances and Li-O bottleneck sizes.

Adding a New Dimension to the Investigation of Platinum-Mediated Arene C−H Activation Reactions Using 2D NMR Exchange Spectroscopy. Dynamics of Pt(II) Phenyl/Benzene Site Exchange

Protonation of (N-N)PtPh(2) (1; N-N = diimine ArN=CMe-CMe=NAr with Ar = 2,6-Me(2)C(6)H(3) (a), 2,4,6-Me(3)C(6)H(2) (b), 4-Br-2,6-Me(2)C(6)H(2) (c), 3,5-Me(2)C(6)H(3) (d), and 4-CF(3)C(6)H(4) (e)) in the presence of MeCN at ambient temperature generates (N-N)Pt(Ph)(NCMe)(+) (2). At -78 degrees C, protonation of 1a yielded (N-N)PtPh(2)(H)(NCMe)(+) (3a), which produced benzene and 2a at ca. -40 degrees C. Protonation of 1a-e in CD(2)Cl(2)/Et(2)O-d(10) furnished (N-N)Pt(C(6)H(5))(eta(2)-C(6)H(6))(+) (4a-e). The pi-benzene complexes 4a-c, sterically protected at Pt, eliminate benzene at ca. 0 degree C. The sterically less protected 4d-e lose benzene already at -30 degrees C. SST and 2D EXSY NMR demonstrate that phenyl and pi-benzene ligand protons undergo exchange with concomitant symmetrization of the diimine ligand, most likely via oxidative insertion of Pt into a C-H bond of coordinated benzene. The kinetics of the exchange processes for 4a-c were probed by quantitative EXSY spectroscopy, resulting in DeltaH() of 70-72 kJ mol(-1) and DeltaS of 37-48 J K(-1) mol(-1). A large, strongly temperature-dependent H/D kinetic isotope effect (9.7 at -34 degrees C; 6.9 at -19 degrees C) was measured for the dynamic behavior of 4a versus 4a-d(10), consistent with the proposed pi-benzene C-H bond cleavage. The fact that the pi-benzene complex 4a is thermally more robust in the absence of MeCN than is the Pt(IV) hydridodiphenyl complex 3a in the presence of MeCN agrees with the notion that arene elimination from Pt(IV) hydridoaryl complexes occurs via Pt(II) pi-arene intermediates that eliminate the hydrocarbon associatively, in this case, promoted by MeCN. Compounds 1a, 1b, 1d, 2a, and 2b have been crystallographically characterized.

Direct Observation of Enhanced Translocation of a Homeodomain between DNA Cognate Sites by NMR Exchange Spectroscopy

A novel approach is presented for studying the kinetics of specific protein-DNA interactions by NMR exchange spectroscopy. The experimental design involves the direct observation of translocation of a homeodomain between cognate sites on two oligonucleotide duplexes, differing by only a single base pair at the edge of the DNA recognition sequence. The single base-pair change perturbs the 1H-15N correlation spectrum of a number of residues, while leaving the affinity for the DNA unchanged. The exchange process has apparent rate constants in the 5-20 s-1 range which are linearly dependent upon the concentration of free DNA. These rates are about 3 orders of magnitude larger than the dissociation rate constant determined by gel shift assays at nanomolar DNA concentrations. The complete NMR exchange data set, comprising auto- and cross-peak intensities as a function of mixing time at five concentrations of free DNA, can be fit simultaneously to a simple model in which protein translocation between DNA duplexes occurs via a second-order process (with rate constants of approximately 6 x 104 M-1 s-1) involving direct collision of a protein-DNA complex with free DNA. This is akin to intersegmental transfer, and a physical model for the process is discussed. Rapid translocation at high concentrations of free DNA observed directly by NMR exchange spectroscopy reconciles the long half-lives of protein-DNA complexes measured by biochemical analysis in vitro with the highly dynamic behavior of such complexes observed in vivo. The relevance of this mechanism to the kinetics of protein-DNA interactions within the cell is discussed.

Formation of Porous Aluminophosphate Frameworks Monitored by Hyperpolarized 129Xe NMR Spectroscopy

The formation of two aluminophosphate frameworks, AlPO4-5 and AlPO4-18, has been monitored using hyperpolarized 129Xe NMR as a probe. The reaction progress from an amorphous phase to AlPO4-5 and its subsequent conversion to AlPO4-18 is observed for xenon adsorbed in samples that have been reacted for varying lengths of time. The extreme sensitivity of 129Xe chemical shifts to local environments of the xenon leads to separate NMR peaks for xenon adsorbed in the two different aluminophosphate frameworks present in a single reaction mixture. For xenon adsorbed in AlPO4-5, an anisotropic 129Xe NMR line shape at δiso ≈ 63 ppm is observed, whereas for xenon in AlPO4-18, a peak with a small anisotropy at δiso ≈ 74 ppm is observed. Grand canonical Monte Carlo simulations provide a theoretical description of xenon adsorbed in the two aluminophosphate frameworks, and the resulting simulated 129Xe NMR line shapes are in good agreement with experimental data. Two-dimensional exchange NMR spectroscopy was used to examine the exchange of xenon between AlPO4-5, AlPO4-18, and bulk xenon gas. The results indicate that the domains of AlPO4-5 are in intimate contact with those of AlPO4-18, facilitating a higher intercrystallite exchange than with the bulk xenon gas.

129Xe NMR study of Xe adsorption on multiwall carbon nanotubes

129Xe NMR spectroscopy has been used to study the adsorption of Xe on multi-wall carbon nanotubes (MWCNT). The results obtained have shown the 129Xe NMR ability to probe the intercrystalline (aggregate) and the inner porosity of CNT. In particular, the effects on porosity of tubes openings by hydrogen exposure and of ball milling were examined. Dramatic changes observed in the 129Xe NMR spectra after moderate ball milling of MWCNTs were attributed to the destruction of the initial intercrystalline pore structure and to the Xe access inside the nanotubes. To examine the exchange dynamics the mixture of as-made and milled MWCNTs was studied with one- and two-dimensional (1D and 2D) 129Xe NMR. The exchange between the interior of milled nanotubes and the aggregate pores of as-made MWCNTs was fast on the NMR acquisition time scale. The Xenon exchange between the interior of the as-made MWCNTs and the large aggregate pores occurred on a longer time scale of 10 ms, as was established by 2D 129Xe NMR exchange spectroscopy. Variable temperature 129Xe NMR data were also discussed and analyzed in terms of the fast exchange approximation.

Bonding in Palladium(II) and Platinum(II) Allyl MeO- and H-MOP Complexes. Subtle Differences via 13C NMR

13C NMR studies have shown that in both Pd(II)- and Pt(II)-allyl (modified-MOP) (MOP = (S)-2-diarylphosphino-1,1‘-binaphthyl) complexes the substituent on the MOP auxiliary can affect how the naphthyl backbone interacts with a metal center. With the MeO-MOP analogue, the metal binds the carbon in a weak η1-fashion, whereas with H-MOP it prefers an η2-binding mode. For the Pt complexes, the 1J(195Pt,13C) values proved to be diagnostic tools. Both modes of bonding afford relatively weak bonds to the metal. Modifying the MOP ligand structure from a PPh2 to a P(3,5-di-tert-butylphenyl)2 analogue can markedly affect the bond distances within the coordination sphere, as indicated by the X-ray structural data for PdCl(η3-C3H5)(modified-MOP). 2-D NMR exchange spectroscopy can be used to recognize and distinguish between the two most common types of η3−η1−η3 isomerization process, i.e., rotation around the allyl C−C bond versus rotation around the allyl M−C bond. For the complex PdCl(η3-C3H5)(H-MOP), the fastest i...

Polyphosphate composite: conductivity and NMR studies

A polyphosphate composite [NH 4PO 3] 6[(NH 4) 2SiP 4O 13] with high ionic conductivity was prepared and characterized by chemical analysis, X-ray diffraction, thermal gravimetry, impedance spectroscopy, and different NMR techniques. Experiments were carried out in dry and humid atmospheres and in temperatures ranging between 20 °C and 300 °C. During initial heating (activation) of the composite to 300 °C, a weight loss of 7% due to release of ammonia occurs resulting in a material of the formal composition of [HPO 3] 3[NH 4PO 3] 3[(NH 4) 2SiP 4O 13]. This material is thermally stable between room temperature and 300 °C. The conductivity was found to be remarkably high (0.1 S cm −1) in a water-rich environment. Mainly ammonium species could be found in the 1H MAS NMR spectra of the non-activated composite, whereas during the activation process another signal due to bridging hydrogen increases. Temperature-dependent 2D and 1D exchange NMR spectroscopy, PFG (pulsed field gradient) NMR, and SFG (stray field gradient) NMR measurements were performed in order to compare diffusion coefficients and exchange rates with dc conductivities. The small differences between experimentally obtained conductivities and those determined from the measured self-diffusion coefficients by means of the Nernst–Einstein equation hints to an ammonium vehicle as charge carrier, but can be also explained by H + conductivity. The slow NMR exchange rates between hydroxyl groups and ammonium ions exclude proton conductivity via hydroxyl groups.

Obmennaya YaMR spektroskopiya tverdogo tela: primenenie dlya izucheniya krupnomasshtabnoi konformatsionnoi dinamiki biopolimerov

Obmennaya YaMR spektroskopiya tverdogo tela: primenenie dlya izucheniya krupnomasshtabnoi konformatsionnoi dinamiki biopolimerov

Hyperpolarized 129Xe NMR spectroscopic investigation of potentially porous shape-persistent macrocyclic materials

The application of continuous-flow hyperpolarized 129Xe NMR spectroscopy to investigate the pores of three shape-persistent organic macrocycles is described. Peaks with xenon chemical shifts between 160 and 200 ppm are assigned to xenon atoms trapped in highly confined pores while NMR peaks with chemical shifts of 100 to 140 ppm are assigned to xenon present in channels that exist through the centre of the stacked macrocycles. With the aid of molecular dynamics simulations, connections between the 129Xe NMR spectra and the X-ray diffraction structure of one of the solvated macrocycles, 1, have been made. The similarities in the 129Xe NMR spectra of the three compounds containing hyperpolarized xenon suggest that all three hosts possess comparable pore structures. The 129Xe NMR data provide information about the porous nature of the two compounds for which X-ray crystallographic analysis was not possible. Data obtained from two-dimensional 129Xe NMR exchange spectroscopy experiments, variable-temperature 129Xe NMR and molecular dynamics simulations suggest a mechanism whereby the xenon gains access to the highly confined sites via the channels.

When electron exchange is chemical exchange–assignment of1H NMR spectra of paramagnetic cobalt(ii)-2,2′:6′,2″-terpyridine complexes

Electron exchange between [Co(terpy)2]3+ and [Co(terpy)2]2+ can be monitored by 1H NMR exchange spectroscopy and allows the cobalt(II) spectra to be fully assigned.

15N Solid-State NMR Characterization of Ammonia Adsorption Environments in 3A Zeolite Molecular Sieves

The quantitative analysis of ammonia binding sites in 3A zeolite molecular sieves using solid-state 15N MAS NMR spectroscopy is reported. By utilizing 15N-enriched ammonia (15NH3) gas, the different adsorption/binding sites within the zeolite were characterized as a function of NH3 loading. Using 15N MAS NMR, multiple sites were resolved that have distinct cross-polarization dynamics, relaxation, and chemical shift behavior. A combination of 15N/23Na and 15N/27Al TRAPDOR NMR methods was used to demonstrate significant dipolar coupling between adsorbed ammonia molecules and both Na cations and Al framework species in the zeolite cage. An estimate of the 23Na−15N and 27Al−15N distance was obtained from simulation of the TRAPDOR results. Two-dimensional 1H → 15N CP-MAS NMR exchange spectroscopy was implemented to probe dynamics between the two primary adsorbed ammonia environments. In the 3A zeolite, the observed exchange process between the ammonia sites does not display a significant temperature dependence...

Olefin Polymerization Promoted by a Stereorigid Bridged Diiminobis(phenolate) Zirconium Complex

Two diiminobis(phenolate) zirconium complexes [C6H10-{NCH-(3,5-tBu2C6H2-2-O)-κO}2]ZrX2 [X = CH2Ph (1), Cl (3)] have been synthesized and characterized by NMR solution spectroscopy. Complex 1 was found conformationally stable and isolated in the octahedral C2 symmetric form. When exposed to the light in hydrocarbon solution, 1 readily undergoes to 1,2 benzyl migration converting the diiminobis(phenolate) ligand in the corresponding benzylamidoiminobis(phenolate). Complex 3 is more thermally stable and found in slow equilibrium between the cis-α and cis-β forms with the former largely prevalent (9:1 molar ratio). The rate of interconversion between the two diastereoisomers was estimated in 3.6 × 10-1 s-1 by NMR exchange spectroscopy (EXSY). 1 and 3 are active ethylene polymerization catalysts after reaction with MAO or [CPh3][B(C6F5)4]/Al-iBu3. The polydispersity index of polyethylene produced by 1 is about 2, suggesting the presence of a single active species and that the symmetry of the precatalyst is ret...

Conformation and orientation of a protein folding intermediate trapped by adsorption.

Although adsorption-induced conformational changes of proteins play an essential role during protein adsorption on interfaces, detailed information about these changes is lacking. To further the current understanding of protein adsorption, in this study, the orientation, conformation, and local stability of bovine alpha-lactalbumin (BLA) adsorbed on polystyrene nanospheres is characterized at the residue level by hydrogen/deuterium exchange and 2D NMR spectroscopy. Most of the adsorbed BLA molecules have conformational properties similar to BLA molecules in the acid-induced molten globule state (A state). A folding intermediate of BLA is thus induced and trapped by adsorption of the protein on the hydrophobic interface. Several residues, clustered on one side of the adsorbed folding intermediate of BLA, have altered amide proton exchange protection factors compared to those of the A state of BLA. This side preferentially interacts with the interface and includes residues in helix C, the calcium binding site, and part of the beta-domain. Local unfolding of this interacting part of the adsorbed protein seems to initiate the adsorption-induced unfolding of BLA. Adsorption-induced protein unfolding apparently resembles more the mechanical unfolding of a protein than the global unfolding of a protein as induced by denaturant, pH, or pressure. 2D macromolecular crowding prevented the minority of adsorbed BLA molecules, which arrived late at the interface, to unfold to the A state. Protein adsorption is a novel and challenging approach to probe features of the free energy landscapes accessible to unfolding proteins.

The Nature of Oxygen Exchange in ZrW2O8 Revealed by Two‐Dimensional Solid‐State 17O NMR.

AbstractFor Abstract see ChemInform Abstract in Full Text.

Isomerization dynamics in homo- and heterochiral atropoisomer copper(I) diimine complexes: a 2D EXSY NMR study.

Two-dimensional exchange NMR spectroscopy has been employed to study the isomerization process of copper(I) complexes formed upon complexation of Cu+ with a racemic mixture of the atropoisomer diimine benzimidazole-pyridine ligands 1-3 and evaluate the configurational stability of the pseudotetrahedral complexes [Cu(1-3)2]PF6. Racemization of the heterochiral isomers RSLambda/RSDelta proceeds through an intramolecular ligand rearrangement on a time scale of about 1.9 s(-1) for 1, 4.4 s(-1) for 2, and 0.3 s(-1) for 3 in CD2Cl2 at room temperature. The intramolecular Lambda/Delta isomerizations in the homochiral diastereoisomers RRDelta/SSLambda and RRLambda/SSDelta of [Cu(1)2]PF6 proceed at room temperature on a time scale of about 0.6 s(-1) for the conversion of RRDelta/SSLambda into RRLambda/SSDelta and 13 s(-1) for the conversion of RRLambda/SSDelta into RRDelta/SSLambda. The kinetics of these intramolecular exchange processes were found to be sensitive to the stabilizing interligand pi-stacking interactions that develop within the [Cu(1-3)2]+ structure and to the bulkiness of the benzimidazole aryl substituents. The kinetics of racemization in the heterochiral RSLambda/RSDelta isomers of [Cu(3)2]PF6 with the bulky cumyl-derived ligand were 1 order of magnitude lower than in [Cu(2)2]PF6 with the tolyl-based ligand. Slower intermolecular ligand exchanges between all the isomers have also been shown to occur at ambient temperature in CD2Cl2 through complete ligand dissociation. Free energies at 298 K varying between 66.7 and 74.4 kJ.mol(-1) and entropies varying between -26.4 and 28.3 J.K(-1).mol(-1) were determined for the intramolecular Lambda/Delta isomerizations. For the intermolecular ligand exchanges free energies at 298 K varying between 55.6 and 62.5 kJ.mol(-1) and entropies varying between -97.9 and -74.5 J.K(-1).mol(-1) were measured.

The nature of oxygen exchange in ZrW2O8 revealed by two-dimensional solid-state 17O NMR.

17O magic angle spinning (MAS) NMR has been used to determine the nature of oxygen exchange in ZrW(2)O(8). A highly effective isotopic labelling technique has been developed and 1D NMR and 2D exchange spectroscopy (EXSY) experiments have revealed that mutual exchange occurs between all oxygen sites, even at temperatures considerably below the alpha to beta order-disorder phase transition.

Orientation Of Tensorial Interactions Determined From Two-Dimensional Nutation Exchange Nqr And Nmr Powder Spectra

The method for determining the mutual orientation of molecular interaction tensors in powders is described. The technique is based on 2D nutation exchange NQR and NMR spectroscopy. It is shown that the 2D nutation exchange spectra exhibit characteristic ridges, which reflect the motional mechanism in a model-independent fashion. The angles through which the molecule rotates can be read from elliptical ridges in the 2D spectra. The 2D nutation exchange NMR and NQR powder patterns are calculated for spins I = 1 and I = 3/2 for different symmetry of reorienting molecular groups.

Ligand Exchange Dynamics in Aluminum Tris-(Quinoline-8-olate): A Solution State NMR Study

The exchange kinetics between the three symmetry-inequivalent ligands in the meridianal isomer of aluminum tris-(quinoline-8-olate) (Alq(3)), a widely used electron-transporting and light-emitting material in the field of organic light emitting diodes, have been studied using two-dimensional exchange NMR spectroscopy in solution. The three inequivalent ligands were found to exchange on a time scale of about 5 s(-)( 1) at room temperature. A simple first-order mechanism based on consecutive 180 degrees flips of the ligands is sufficient to quantitatively explain the experimental data. Activation enthalpies between 83 and 106 kJ mol(-)( 1) were found for the flips of the three inequivalent ligands. The activation entropies are positive, suggesting a highly disordered transition state. These findings elucidate the internally mobile nature of the Alq(3) complex, and may have important implications for the morphology of vapor deposited thin films of Alq(3) as well as for crystallization-assisted device failures.

High-Resolution Solid-State NMR Studies of Imidazole-Based Proton Conductors: Structure Motifs and Chemical Exchange from 1H NMR

High-resolution solid-state 1H NMR under fast magic angle spinning is used for the first time to study proton conductivity. The materials of interest, ethylene oxide tethered imidazole heterocycles (Imi-nEO), are characterized by variable temperature experiments, as well as 2D homonuclear double quantum (DQ) NMR and 2D exchange spectroscopy. Quantum chemical calculations provide a full assignment and understanding of the 1H chemical shifts, based on a single-crystal structure obtained for Imi-2EO. Three types of hydrogen-bonded N-1H resonances are observed by 1H MAS NMR at 30 kHz. Double quantum NMR experiments identify those hydrogen-bonded protons that are mobile on the time scale of the experiment, and thereby, those which are able to participate in charge transport. Characterized by their spin−spin relaxation ( ) behavior, the local mobility of these protons as a function of temperature is compared to the conductivity of the materials. Homonuclear 1H 2D DQ MAS spectra provide evidence for locally ordered domains within all the Imi-nEO materials. Disordered (mobile) and ordered components in Imi-2EO dramatically differ in their 1H spin−lattice relaxation times. 2D NOESY spectra show no evidence of chemical exchange processes between the ordered and disordered domains. These results indicate that the highly ordered regions of the materials do not (or only poorly) contribute to proton conductivity, which is rather taking place in the disordered regions. Molecules in the disordered domains are in a state of dynamic or fluctuating hydrogen-bonding, allowing for Grotthus mechanism proton transport, while molecules in the ordered domains do not experience exchange, and do not participate in long-range proton conductivity. At the interface between these regimes a small number of molecules undergo slow exchange. With increasing temperature, this exchange becomes fast on the NMR time scale, and the final chemical shift of 12.5 ppm in Imi-5EO implies the persistence of strongly and weakly hydrogen-bonded domains, which reorganize rapidly to support the proton transport process.