Structure dipolar coupling

Figure 1 The principal sources of structural data are the NOEs, which give information on the spatial proximity d of protons coupling constants, which give information on dihedral angles < i and residual dipolar couplings, which give information on the relative orientation 0 of a bond vector with respect to the molecule (to the magnetic anisotropy tensor or an alignment tensor). Protons are shown as spheres. The dashed line indicates a coordinate system rigidly attached to the molecule.

A similar problem arises with present cross-validated measures of fit [92], because they also are applied to the final clean list of restraints. Residual dipolar couplings offer an entirely different and, owing to their long-range nature, very powerful way of validating structures against experimental data [93]. Similar to cross-validation, a set of residual dipolar couplings can be excluded from the refinement, and the deviations from this set are evaluated in the refined structures. 

Molecular modeling is an indispensable tool in the determination of macromolecular structures from NMR data and in the interpretation of the data. Thus, state-of-the-art molecular dynamics simulations can reproduce relaxation data well [9,96] and supply a model of the motion in atomic detail. Qualitative aspects of correlated backbone motions can be understood from NMR structure ensembles [63]. Additional data, in particular residual dipolar couplings, improve the precision and accuracy of NMR structures qualitatively [12]. 

Instead of measuring only the time-dependent dipolar interaction via NOE, it is also possible to determine dipolar couplings directly if the solute molecule is partially aligned in so-called alignment media. The most important resulting anisotropic parameters are RDCs, but residual quadrupolar couplings (RQCs), residual chemical shift anisotropy (RCSA) and pseudo-contact shifts (PCSs) can also be used for structure determination if applicable. 

Simon, B., Sattler, M. De novo structure determination from residual dipolar couplings by NM R spectroscopy. Angew. Chem. Int. Ed. 2002, 41, 437 40. 

Kniep R, Simon P (2007) Fluorapatite-Gelatine-Nanocomposites Self-Organized Morphogenesis, Real Structure and Relations to Natural Hard Materials. 270 73-125 Koenig BW (2007) Residual Dipolar Couplings Report on the Active Conformation of Rhodopsin-Bound Protein Fragments. 272 187-216 Kolusheva S, see Jelinek R (2007) 277 155-180... 

Olejniczak ET, Meadows RP, Wang H, Cai M, Nettesheim DG, Fesik SW. Improved NMR structures of protein/ligand complexes using residual dipolar couplings. J Am Chem Soc 1999 121 9249-9250. 

Shortle has focused on the unfolded state for more than a decade, leading up to his recent demonstration using residual dipolar couplings that staphylococcal nuclease retains global structure in 8 M urea. His chapter on The Expanded Denatured State sets the stage. Dunker etal. then explore the complementary world of disordered regions within... 

The most important feature of the information in dipolar couplings is that it is independent of distance. The data can be envisioned as reflecting the relative orientation of pairs of bond vectors, with the intervening distance having no effect (Meiler et al., 2000). Thus dipolar couplings can potentially provide a method for characterizing the structure of denatured proteins, provided that the denatured state ensemble of conformations retains several levels of nonrandomness. 

Conversion of dipolar coupling data into three-dimensional structures presents a major challenge for folded proteins and for not-folded proteins, an additional set of obstacles must be confronted (Ackerman and Shortle, 2002). Nevertheless, the correlation of dipolar couplings measured under two sets of conditions establishes that the structures are likely to be highly similar. 

Fig. 14. (A) Ac-L-Ala-NHMe structure with best-fit dipolar coupling constants (Hz).

Each of these couplings is inversely proportional to the cube of the distance between the atoms concerned, and all the dipolar couplings depend on the degree of orientation of the molecules. The ratios of couplings thus depend on the ratios of distances in the molecule, and from them the entire molecular structure, except for the overall size, may be determined. Studies of silyl compounds dissolved in cyanobiphenyl liquid crystals have yielded the following HSiH angles ... 

In the solid, dynamics occurring within the kHz frequency scale can be examined by line-shape analysis of 2H or 13C (or 15N) NMR spectra by respective quadrupolar and CSA interactions, isotropic peaks16,59-62 or dipolar couplings based on dipolar chemical shift correlation experiments.63-65 In the former, tyrosine or phenylalanine dynamics of Leu-enkephalin are examined at frequencies of 103-104 Hz by 2H NMR of deuterated samples and at 1.3 x 102 Hz by 13C CPMAS, respectively.60-62 In the latter, dipolar interactions between the 1H-1H and 1H-13C (or 3H-15N) pairs are determined by a 2D-MAS SLF technique such as wide-line separation (WISE)63 and dipolar chemical shift separation (DIP-SHIFT)64,65 or Lee-Goldburg CP (LGCP) NMR,66 respectively. In the WISE experiment, the XH wide-line spectrum of the blend polymers consists of a rather featureless superposition of components with different dipolar widths which can be separated in the second frequency dimension and related to structural units according to their 13C chemical shifts.63... 

Other exciting applications involved using parallel tempering in connection with available experimental data. For example, Falcioni and Deem [57] used X-ray data to refine structures of zeolites, and Haliloglu et al. [58] refined NMR structural data for proteins (in particular using residual dipolar coupling constraints). 

Haliloglu, T. Kolinski, A. Skolnick, J., Use of residual dipolar couplings as restraints in ab initio protein structure prediction, Biopolymers 2003, 70, 548-562... 

When a molecule exhibits large internal motions difficulties arise in using most available techniques for the determination of molecular geometry. In a study of 2,2 -biselenophene it was shown that although internal motion is present, useful structural information can still be obtained in the liquid crystal phase and that, at present, other techniques are not available for obtaining equivalent information, at least not in a liquid-like phase.13 This study also demonstrates the usefulness of the heteroatom satellites, and in particular of Se—H dipolar couplings. 

The isotropic chemical shift, the trace of the chemical shift tensor, is one of the basic NMR parameters often measured for both spin-1/2 and quadrupolar nuclei. The CSA can also be measured in non-cubic environments, such as the n3Cd nuclei experience in the chalcopyrite structure of crystalline CdGeAs2 [141] or CdGeP2 [142], and the 31P nuclei in the latter compound [142], Although the isotropic chemical shift can be measured from the NMR spectrum of a static powder because the CSA is zero in many cases because of cubic symmetry of the lattice, improved resolution is obtained by using MAS to remove dipolar couplings. Two particular areas where the isotropic chemical shifts have proven very informative will now be discussed, semiconductor alloys and semiconductor polytypes. 

Finally, a series of papers have been published on the solid state NMR spectra of a number of analgesic drugs. Jagannathan recorded the solid state 13C NMR spectrum of acetaminophen in bulk and dosage forms [60], From the solution-phase NMR spectrum, assignments of the solid state NMR resonances could be made in addition to explanations for the doublet structure of some resonances (dipolar coupling). Spectra of the dosage product from two sources indicated... 

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