Composite spectral density functions for the interpretation of the 13C NMR relaxation behavior of polymers containing hydrocarbon side chains. Free and restricted side chain motion

¹³C NMR NT₁ and NOE have been calculated by using composite spectral density functions describing polymer chain segmental motion and internal rotation of a hydrocarbon side chain attached to the polymer backbone. Numerical results at two magnetic fields are presented as a function of the various motional parameters characterizing the various models. NT₁ and NOE relaxation parameters are well behaved and appear to have practical value for describing the dynamics of these systems. The models have been applied to the relaxation data of poly(n-butyl methacrylate) and poly(n-hexyl methacrylate) in toluene solutions. The dynamics of the two polymers are characterized by a very localized backbone motion and restricted internal rotation about successive C? C bonds of the side chains. © 1995 John Wiley & Sons, Inc.     

Local chain motions of poly(β-hydroxyoctanoate) in the bulk. 13C NMR relaxation study

Variable-temperature ¹³C NMR spin-lattice relaxation times (T₁) and Nuclear Overhauser Enhancements (NOE) at two magnetic fields have been used to study the dynamics of the amorphous part of a semicrystalline sample (33% of crystallinity) of poly(β-hydroxyoctanoate) (PHO). The interpretation of the relaxation data of the backbone carbons was made by employing a number of motional models. Among these, the DLM model offered the best interpretation of the relaxation data in terms of conformational transitions and librational motions of the backbone C? H vectors, and proved to be superior to unimodal distribution functions. The interpretation of temperature- and frequency-dependent T₁ and NOE data of the carbon nuclei in the n-pentyl side chain was made by employing a newly developed composite spectral density function for multiple internal C? C bond rotations of restricted amplitude and chain segmental motion. The temperature dependence of the linewidths of the various protonated carbon resonances of PHO has been discussed in terms of the semicrystalline character of this polymer. © 1995 John Wiley & Sons, Inc.     

Examination of intermediates in globular protein unfolding by the tritium labeling method

Unfolding of polypeptide chain of ribonuclease A in urea and guanidinium chloride (GuCl) solutions under equilibrium conditions involves formation of intermediates whose properties (compactness and preservation of the most of the native hydrophobic core, secondary structures, and native-like folding of the polypeptide chain) correspond to the basic characteristics of the “molten globule” state. Intermediates are “damp” molten globules (with water molecules inside the globule). The examinations performed revealed pronounced distinctions in the properties of the intermediates, above all, in their compactness degrees.     

NMR conformational analysis of antide, a potent antagonist of the gonadotropin releasing hormone

Antide is a decapeptide [(N-Ac-D-Nal(1)-D-Cpa(2)-D-Pal(3)-Ser(4)-Lys(Nic)(5)-D-Lys(Nic)(6)-Leu(7)-Ilys(8)-Pro(9)-D-Ala(10)-NH(2)] that acts in vivo as an antagonist of GnRH (gonadotropin-releasing hormone). The conformational behavior of antide has been studied in water, TFE, DMF, and DMSO solutions by means of 2D-NMR spectroscopy and molecular dynamics calculations. Antide adopts in aqueous solution a delta-shaped backbone conformation, which is characterized by an irregular turn around residues D-Pal(3)-Ser(4) and by the close spatial proximity of the side chains belonging to D-Nal(1) and Ilys(8) (as many as 17 NOE peaks were detected between these side chains). The side-chain protons of Ilys(8) (especially the H(gamma) ones) present remarkably upfield shifted resonances, because of ring current effects induced by the naphthyl moiety. The upfield shifted resonances of the Ilys(8) H(gamma) hydrogen atoms are strictly characteristic of the water delta-shaped conformation and can be considered as structure markers. The observation of ring current shifted Ilys(8) H(gamma) resonances under different conditions (temperature, pH, solvent) indicates a remarkable stability of the water delta-shaped conformation. Such a conformation is at least partially disrupted in solvent mixtures containing high percentages of organic solvents. TFE can induce a well-defined conformation, which is characterized by an S-shaped backbone conformation. In DMF and DMSO solution, the molecule is basically endowed with a random coil conformation and high fluxionality. Antide fulfills the conformational requirements that are known to play a crucial role in receptor recognition, namely (i) the presence of a turn in the backbone and (ii) the all-trans nature of peptide bonds. In addition, the structural rigidity of antide likely adds a further contribution to the receptor binding affinity.     

Temperature dependence of domain motions of calmodulin probed by NMR relaxation at multiple fields

Interdomain motions of Ca(2+)-ligated calmodulin were characterized by analyzing the nuclear magnetic resonance (15)N longitudinal relaxation rate R(1), transverse relaxation rate R(2), and steady-state {(1)H}-(15)N NOE of the backbone amide group at three different magnetic field strengths (18.8, 14.1, and 8.5 T) and four different temperatures (21, 27, 35, and 43 degrees C). Between 35 and 43 degrees C, a larger than expected change in the amplitude and the time scale of the interdomain motion for both N- and C-domains was observed. We attribute this to the shift in population of four residues (74-77) in the central linker from predominantly helical to random coil in this temperature range. This is consistent with the conformation of these residues in the calmodulin-peptide complex, where they are nonhelical. The doubling of the disordered region of the central helix (residues 78-81 at room temperature) when temperature is raised from 35 to 43 degrees C results in larger amplitude interdomain motion. Our analysis of the NMR relaxation data quantifies subtle changes in the interdomain dynamics and provides an additional tool to monitor conformational changes in multidomain proteins.     

The mobile proton in polyalanine peptides

Ion mobility measurements have been performed for protonated polyalanine peptides (A10 + H+, A15 + H+, A20 + H+, A25 + H+, and A15NH2 + H+) as a function of temperature using a new high-temperature drift tube. Peaks due to helices and globules were found at room temperature for all peptides, except for A10 + H+ (where only the globule is present). As the temperature is increased, the helix and globule peaks broaden and merge to give a single narrow peak. This indicates that the two conformations interconvert rapidly at elevated temperatures. The positions of the merged peaks show that A15 + H+ and A15NH2 + H+ spend most of their time as globules when heated, while A20 + H+ and A25 + H+ spend most of their time as helices. The helix/globule transitions are almost certainly accompanied by intramolecular proton transfer, and so, these results suggest that the proton becomes mobile (able to migrate freely along the backbone) at around 450 K. The peptides dissociate as the temperature is increased further to give predominantly the bn(+), b(n-1)(+), b(n-2)(+), ... series of fragment ions. There is a correlation between the ease of fragmentation and the time spent in the helical conformation for the An + H+ peptides. Helix formation promotes dissociation because it pools the proton at the C-terminus where it is required for dissociation to give the observed products. In addition to the helix and globule, an antiparallel helical dimer is observed for the larger peptides. The dimer can be collisionally dissociated by injection into the drift tube at elevated kinetic energies.     

Temperature dependence of anisotropic protein backbone dynamics

The measurement of (15)N NMR spin relaxation, which reports the (15)N-(1)H vector reorientational dynamics, is a widely used experimental method to assess the motion of the protein backbone. Here, we investigate whether the (15)N-(1)H vector motions are representative of the overall backbone motions, by analyzing the temperature dependence of the (15)N-(1)H and (13)CO-(13)C(alpha) reorientational dynamics for the small proteins binase and ubiquitin. The latter dynamics were measured using NMR cross-correlated relaxation experiments. The data show that, on average, the (15)N-(1)H order parameters decrease only by 2.5% between 5 and 30 degrees C. In contrast, the (13)CO-(13)C(alpha) order parameters decrease by 10% over the same temperature trajectory. This strongly indicates that there are polypeptide-backbone motions activated at room temperature that are not sensed by the (15)N-(1)H vector. Our findings are at variance with the common crank-shaft model for protein backbone dynamics, which predicts the opposite behavior. This study suggests that investigation of the (15)N relaxation alone would lead to underestimation of the dynamics of the protein backbone and the entropy contained therein.     

Structure of pyrimidinocyclophanes in solution by NMR

The conformations and self-associative properties of novel pyrimidinocyclophanes with a substituted nitrogen atom in a spacer have been studied using several independent NMR methods (NOE, aromatic shielding effect, 2D DOSY, GIAO DFT chemical shift calculations, DNMR) in a variety of solvents, in acidic and basic media. At room temperature the title compounds in neutral solution are in slow exchange on the NMR time-scale and exist in a folded conformation. In the acidic medium protonation occurs at the bridge nitrogen, and that leads to dramatic modifications of the structure and dynamics of the compound. The protonated form exists at the equilibrium of ‘folded’ and ‘extended’ conformers. Moreover, the protonated form is prone to association and can be effectively described as a dimer at room temperature.     

Direct use of unassigned resonances in NMR structure calculations with proxy residues

We present a method that significantly enhances the robustness of (automated) NMR structure determination by allowing the NOE data corresponding to unassigned NMR resonances to be used directly in the calculations. The unassigned resonances are represented by additional atoms or groups of atoms that have no interaction with the regular protein atoms except through distance restraints. These so-called "proxy" residues can be used to generate NOE-based distance restraints in a similar fashion as for the assigned part of the protein. If sufficient NOE information is available, the restraints are expected to place the proxies at positions close to the correct atoms for the unassigned resonance, which can facilitate subsequent assignment. Convergence can be further improved by supplying additional information about the possible identities of the unassigned resonances. We have implemented this approach in the widely used automated assignment and structure calculation protocols ARIA and CANDID. We find that it significantly increases the robustness of structure calculations with regard to missing assignments and yields structures of higher quality. Our approach is still able to find correctly folded structures with up to 30% randomly missing resonance assignments, and even when only backbone and beta resonances are present! This should be of significant value to NMR-based structural proteomics initiatives.     

Deuterium quantification through deuterium-induced remote 1H and 13C NMR shifts

Partial labeling by deuterium may be quantified through simple integrations of those (1)H (200 or 400?MHz) and (13)C (100.6?MHz) NMR resonances that are split into pairs by chemical shifts (n)Δ = δ(deuterated) - δ(nondeuterated) as induced by deuterium across n>2 chemical bonds. The relative intensities of the two components of a pair are shown to be influenced to practically equal degrees by relaxation effects, so that a deuterium fraction may be determined from (1)H and (13)C integral pairs at more remote molecular positions under the routine conditions of fast accumulative spectral acquisition.     

Acyclic, achiral enamide nucleoside analogues. The importance of the C=C bond in the analogue for its ability to mimic natural nucleosides

The conformations of an acyclic, achiral enamide thymidine analogue 1 have been studied by model building and geometry calculations, as well as by NMR NOE and UV experiments. The results indicate that there are no significant barriers to rotation around any of the sigma bonds, in particular the N1-C1' enamide bond, and that the analogue should be able to accommodate conformations that mimic the conformations of natural nucleosides in A- and B-type helices quite well. For comparison the saturated analogue 2 has been prepared and built into oligonucleotides. It is shown that incorporation of 2 in oligonucleotides results in a much larger depression of the melting temperature (deltaTm -10 to -12.5 degrees C) than does incorporation of 1 (deltaTm -5 to -6.5 degrees C).     

Perturbation of conjugation in internally solvated allylic lithium compounds: variation of ligand structure. NMR and X-ray crystallography

Several allyic lithium compounds were prepared with different potential ligands tethered at C2. These are with CH3OCH2CH2NCH3CH2-, 5 and 1-TMS 6, with (CH3)2NCH2CH2NCH3CH2-, 1-TMS 7, and with ((CH3)2NCH2CH2)2NCH2-, 8 and 1-TMS 9. In all these compounds Li is fully coordinated to the pendant ligand and is sited off the axis perpendicular to the allyl plane at one of the allyl termini as indicated by a combination of X-ray crystallography and NMR spectra. Compounds 5 and 8 are Li-bridged dimers as shown by X-ray crystallography and also dimeric in benzene solution as determined from freezing point determinations. Compounds 6, 7, and 9 are monomeric in THF-d8 or diethyl ether-d10 solution and exhibit one bond 13C1, 6Li scalar coupling at low temperature. Taken together the crystallographic and NMR data indicate that all of these compounds incorporate partially delocalized allylic moieties. Compounds 5 and 8 undergo fast 1,3-Li-sigmatropic shifts that are proposed to take place within low concentrations of monomers in fast equilibrium with prevalent dimers. Averaging with increasing temperature of the one-bond 13C, 6Li coupling constant in 6, 7, and 13 provided the dynamics of bimolecular C-Li exchange with Delta H++ values of 6.7, 12, and 13 kcal x mol(-1), respectively. Averaging of the diastereotopic N(CH3)2 13C resonances of 7 is indicative of fast transfer of coordinated ligand between faces of the allyl plane Delta H++ = 5.3 kcal x mol(-1) combined with slower inversion at nitrogen. Compound 8 exhibits similar effects. It is concluded that variation of the ligand structure changes dynamic behavior of the compounds but has little influence of their degrees of delocalization.     

Low-temperature 1H and 13C NMR spectra of N-substituted 1,2,3,4-tetrahydropyrazino[1,2-a]indoles

The temperature-dependent (1)H and (13)C NMR spectra of 2-(2-butynyl)-10-methyl-1,2,3,4-tetrahydropyrazino[1,2-a]indole (4) (as a representative example of 1-9) in CFCl(3) + CD(2)Cl(2) solution are described and discussed. Below 183 K, the hexahydropyrazine ring inversions become slow on the NMR time-scale and 4 exists in principle as two conformational diastereomers. In fact, only one was observed with the N-2 substituent in an equatorial position as shown by a low-temperature NOESY experiment. The energy barrier for conformational interchange was calculated from NMR data to be 8.3 kcal mol(-1) (1 kcal = 4.184 kJ), in agreement with quantum chemical calculations. Unambiguous assignments for all proton and carbon resonances of 1-9 were made using 1D (APT, DEPT, NOE difference) and 2D (COSY, NOESY, gHMQC, gHMBC) NMR techniques.     

17O NMR in room temperature phase of La2Mo2O9 fast oxide ionic conductor

A room temperature (17)O NMR study of La(2)Mo(2)O(9), a fast oxide ionic conductor exhibiting a phase transition at 580 degrees C between a low-temperature alpha-phase and a high-temperature beta-phase, is presented. Four partly overlapping quasi-continuous distributions of oxygen sites are evidenced from 1D magic angle spinning (MAS) and 2D triple quantum MAS NMR experiments. They can be correlated with the three oxygen sites O1, O2 and O3 of the high-temperature crystal structure. The low-temperature phase is characterized by two distributed sites of type O1, which proves that the symmetry is lower than in the cubic high-temperature phase. Two-dimensional experiments show that there is no dynamic exchange process, on the NMR time-scale, between the different oxygen sites at room temperature, which agrees well with conductivity results.     

Aib-rich peptides containing lactam-bridged side chains as models of the 3(10)-helix.

Aib-rich side chain lactam-bridged oligomers with n =1, 2, 3, were designed and synthesized as putative models of the 3(10)-helix. These peptides were conformationally characterized in aqueous solution containing SDS micelles by CD, NMR, and computer simulations. The lactam bridge between the side chains of L-Glu and L-Lys in (i) and (i+3) positions was introduced in order to enhance the conformational preference toward the right-handed 3(10)-helix. The NMR results clearly indicate that there is an increase of 3(10)-helix formation upon chain elongation. In the dimer and trimer (n = 2 and n = 3, respectively, in the structure reported above) the observed NOE connectivities are compatible with the 3(10)-helical arrangement, confirmed by the temperature coefficients of the amide proton resonances which suggest the presence of a hydrogen-bonded structure. The phi and psi dihedral angles of the structures obtained by molecular dynamics calculations are also compatible with the 3(10)-helix. Identification of the hydrogen-bond pattern indicate that C=O(i)- - -HN(i+3) hydrogen bonds, typical of the 3(10)-helical conformation, are highly probable in all low-energy structures. The CD spectra of these Aib-rich lactam-bridged oligopeptides, obtained in the same solvent system used for NMR experiments, provide important insight into the spectroscopic characteristics of the 3(10)-helix.     

Comment on “spin decoupling by torsional transitions”

A re-examination of the 220 MHz ¹H NMR spectra of N-(2-hydroxythiobenzoyl)morpholine provides no support for a previous proposal involving spin decoupling by torsional transitions. At ambient temperature, rotation around both the C(S)N and the phenylC(S) bonds occurs at a rate comparable with the NMR time-scale.     

Application of the model‐free approach to low molecular weight systems with hindered internal rotation: cinnamoylmesitylene

We investigated the molecular dynamics of the molecule of cinnamoylmesitylene, a substituted chalcone. Known rotation barriers for the O?C‐4—C‐3?C‐2 bond of substituted chalcones are in the range of values accessible to modern NMR techniques. The internal rotation about the C‐3—C‐4 bond is found to be fast relative to the complete lineshape analysis (CLSA) time‐scale. To determine the activation parameters of overall and internal motions of the molecule, the Lipari–Szabo model‐free analysis of the relaxation times and heteronuclear NOE data was used instead. Simultaneous analysis of both heteronuclear spin–lattice relaxation times and NOE data for the two carbon atoms C‐2 and C‐7 in the O?C‐4—C‐3?C‐2 and mesitylene fragments at different temperatures was performed. The correlation times and activation energies of overall and internal motions and the generalized order parameter, which are measures of the molecular mobility, were thus determined. The standard enthalpies of activation, ΔH^≠, calculated from the experimental data for C‐2 and C‐7, are 5.6 and 6.6 kcal mol^?1, respectively. Theoretical estimates of the barriers to internal rotations by ab initio MO calculations were made to verify the experimental results. The agreement between the NMR and theoretical results was good. Copyright © 2003 John Wiley & Sons, Ltd.     

Spectroscopic and computational investigations of stable radical anions of triosmium benzoheterocycle clusters

The variable temperature (1)H and (13)C NMR and EPR spectra of the stable radical anions [Os(3)(CO)(9)(micro(3)-eta(2)-L)(micro-H)] (LH=phenanthridine, 1; 5,6-benzoquinoline, 2), and [Os(3)(CO)(10)(micro(3)-eta(2)-L)(micro-H)] (LH=quinoxaline, 3) are reported. The radical anions 1(-), 2(-), and 3(-) can be prepared by both exhaustive electrolysis and partially by chemical reduction with cobaltocene and with sodium dispersion (only with sodium dispersion in the case of 3(-)). DFT calculations on 1-3 reveal that the LUMO for the electron-deficient compounds 1 and 2 involves significant contributions from both the heterocyclic ligand and the two metal atoms bridged by the ligand and the micro-hydride. The character of this orbital rationalizes the previously observed regioselective reactions of these complexes with nucleophiles. In contrast, the LUMO for the electron precise 3 involves only ligand-based orbitals. Partial chemical reduction of 1 and 2 requires an excess of either cobaltocene or sodium, and their (1)H and (13)C NMR spectra reveal selective line broadening of those proton resonances that are predicted by DFT calculations to bear the greatest amount of free spin density. The variable temperature behavior of the partially chemically reduced species of 1 and 2 indicates that electron transfer between the reduced/unreduced cluster pair and between the cobaltocene/cobaltocenium pair occurs on the NMR timescale. The radical anions of 1 and 2 prepared by exhaustive electrolysis show an EPR signal at room temperature, while the NMR signals are uniformly broadened. Compound 3 appears to be partially reduced by sodium at room temperature and shows uniformly broadened (1)H NMR resonances at room temperature that sharpen significantly at -80 degrees C. The temperature dependence of the spectra are discussed in terms of the effects of relative electron nuclear relaxation processes, chemical exchange, and the results of the DFT calculations.