NMR conformation

Detailed NMR conformational analysis of y -peptides 139-141 (Fig. 2.35) in pyri-dine-d5 revealed that y-peptides as short as four residues adopt a 2.6-hehcal fold stabilized by H-bonds between C=0 and NH +3 which close 14-membered pseudocycles [200, 201]. The 2.614-helical structure of a low energy conformer of y-hex-apeptide 141 as determined from NMR measurements in pyridine-d5 [200], is shown in Fig. 2.36A and B). Determination of the structure of y" -peptides in CD3OH was hampered by the much lower dispersion of the diasterotopic H-C(a) protons compared to their dispersion in pyridine-d5. However, the characteristic and properly resolved i/ir-2 NOE crosspeacks between H-C(y) and NH +2 in the NH/H-C(y) region of the ROESY spectrum were an indication that the 2.6-helical structure is at least partially populated in CD3OH. 

Chattopadhayaya,. An NMR conformational smdy of the complexes of C/ H double-labeled 2 -deoxynucleosides and deoxycytidine kinase (dCK)./. Chem. Soc. Perkin. 

Convert, O. Mazaleyrat, J.-P. Wakselman, M. Morize, I. Reboud-Ravaux, M. NMR conformational analysis of cyclopeptidic substrates of serine proteases, containing an ortho or meta aminobenzoic acid residue. Biopolymers 1990, 30, 583-591. 

Mrestani-Klaus C, Brandt W, Schmidt R, Neubert K, Schiller PW. Proton NMR conformational analysis of cyclic (Vcasomorphin analogues of the type Tyr-cyclo[-N -D-Om-Xaa-Gly-]. Arch Pharm Pharm Med Chem 1996 329 133-142. 

In principle every compound with an amino and a carboxy group can be used for such purpose ranging from simple co-amino acids [e.g., 5-aminopentanoic acid (6-aminovaleric acid) (1, n = 3)]1541 or 6-aminohexanoic acid (e-aminocaproic acid) (1, n = 4)]135,57,4 791 and related derivatives of 3-aminobenzoic acid 14801 or more sophisticated structures. A few examples (1-6) are shown in Scheme 28. Numerous cyclic turn mimetics have been developed in the past years and for details on this subject the reader is directed to Vol. E 22c, Section 12. To explore the rigidification introduced by nonnatural amino acids or equivalent structures into cyclic peptides, a careful NMR conformational analysis is required, since frequently the so-called p-turn mimetics do not enable such turns to be established, conversely other secondary structure elements may be induced.14811... 

Synthesis and Variable-Temperature H NMR Conformational Analysis of Bis(ri5-cyclopentadienyl)titanium Pentasulfide 151... 

Carbon-13 and Proton NMR Conformational Studies of Nitrogen Heterocycles H. Booth, Kem.-Kemi, 1980, 7, 5-10. 

The bound conformation (Fig. 32) was determined from tr-NOESY data and restrained simulated annealing calculations. The NMR-derived bioactive conformation resembles the crystal structure of free hemiasterlin methyl ester [140], The main difference is the displacement of the aromatic ring due to a rotation of 60° of its bonding axis. Besides, the NMR conformation is more compact than the X-ray structure. 

Conformational analyses of JOM-13 and [L-Ala3]DPDPE have proven to be critical for the determination of the bioactive conformation of enkephalin-like peptides at the delta receptor. H-NMR studies of JOM-13 in aqueous solution revealed that this tetrapeptide exists in two distinct conformations on the NMR time scale as evidenced by two sets of resonances [63]. Large differences in the observed chemical shifts and coupling constants for the D-Cys2 residue in the two conformers suggested that the major differences between the two NMR conformers reside in the disulfide portion of the molecule however, a paucity of conformationally informative nuclear Overhauser enhancement (NOE) interactions precluded the development of a detailed structural model from the NMR studies. In order to develop such a model a thorough conformational analysis of JOM-13 was undertaken, in which the NMR data were complemented by x-ray diffraction results and by molecular mechanics calculations [64]. The results indicate that the 11-... 

Lipid bilayers have been studied in vesicles of about 500 A diameter. The bilayers can be made of many lipids. The most common lipid is lecithin, phosphatidyl choline (PC). Packing the lipids in the vesicle results in two-thirds of the lipid head groups on the external face about one-third on the internal face. The head group of the lipid PC is phosphocholine -O-POJ-O-CH2-CH2N (013)3 and the head group is studied by P, H, D or C NMR and the long fatty chains by C, H, or D NMR. Conformational studies of the molecules by conventional de-coupling, nuclear Overhauser effects and by Ln(III) probes... 

These distances, of course, were derived from the NMR conformational analysis. 

One test of this proposed two-step charge recombination is provided by triad 8. In this molecule, the quinone moiety has been moved from the 5,15 relationship to the carotenoid as in 4 to the 5,10 relationship. Thus, the carotenoid and quinone species have been brought much closer together. This has been demonstrated by the NMR conformational studies of both molecules [27], If recombination of C -P-Q were to occur by a direct electron transfer as per step 5 in Figure 9, this change should lead to a large increase in the recombination rate. However, as seen in Table 2, triads 4 and 8 have identical charge separation lifetimes, within experimental error, as would be expected from the two-step mechanism. 

Table IV. NMR conformational analysis of some phenylethylamines. (a) fb = free base.

Cisproline(i-l)-aromatic(i) interactions have been detected in several short peptides in aqueous solution by analysis of anomalous chemical shifts measured by H-NMR. Conformational preferences of esters of 2,2,5,7,8-penta-methylchroman-6-ol were studied by dynamic C NMR in solution and the cross-polarization (CP)-magic angle spinning (MAS) technique in the solid phase. Experimental untilsyn ratios, N NMR chemical shift, and UV) and theoretical [DFT, MP2 and QCISD(T) calculations of optimized structures and untilsyn ratios and free energy differences, and GIAO calculation of NMR chemical shifts] results establish the conformations of iS-nitrosothiols. The formation of the cytosine-uracil (C-U) base pair in a duplex was observed in... 

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