Assignment ambiguous

Figure 6 Steps in automated assignment. (1) Select the lowest energy structures from iteration / — 1 that are used to interpret the spectra. (2) For each peak, list all possible assignments compatible with the resonances within a frequency mnge. (3) Extract a distance for each assignment possibility from the ensemble of structures. (4) Use the distances to assign ambiguous NOEs. (5) Calibrate the peak volumes to obtain distance restraints. (6) Calculate structures based on the new restraints.

Correcting inconsistencies, such as prescribing the wrong bond order between atoms in some molecules, as well as assigning ambiguous names in others ... 

Reports on the triterpene composition of Baccharis genus are recorded in the literature. Baccharis oxide, Fig. (21) is a common and unique triterpene found in many Baccharis species, such as Baccharis halimifolia L. [54] and B. salicifolia [55], The NMR spectra of this compound was assigned ambiguously [56], but recently Nurnberg et al. [57] established the total NMR chemical shift assignments of baccharis oxide. 

INDO calculation of coupling constants, discussion of conformation. > - ) Assignment ambiguous, performed by comparison with other allylic radicals. i <) INDO calculation of coupling constants. ... 

Hiickel, McLachlan, and INDO calculations of spin densities, discussion of conformation. ) Hiickel and McLachlan calculations of coupling constants, for different twist angles at the C(4)-C(S) bond, discussion of contribution from hyperconjugation in aH<4v ) Hiickel and McLachlan calculations of spin densities for s-i-is- and. s-frnn.s-conformations. " ) Assignment ambiguous, based on INDO calculation. ") Hiickel, McLachlan PPP and INDO calculations of spin densities. ... 

Benzisoxazoles, also called anthranils as derivatives of anthranilic acid, are most commonly formed by the closure of bonds C(l)—C(2) or C(2)—C(3), or the introduction of atom C(3) resulting in formation of bonds C(2)—C(3) and C(3)—C(3a). As with the 1,2-benzisoxazole series, many early structural ambiguities were present in assignments (67AHC(8)277, 62HC(17)1, 66Dis(B)102). The 3-hydroxy compound is primarily in the keto form and only recently have ethers been reported. 

In an isolated two-spin system, the NOE (or, more accurately, the slope of its buildup) depends simply on where d is the distance between two protons. The difficulties in the interpretation of the NOE originate in deviations from this simple distance dependence of the NOE buildup (due to spin diffusion caused by other nearby protons, and internal dynamics) and from possible ambiguities in its assignment to a specific proton pair. Mofec-ufar modeling methods to deaf with these difficulties are discussed further below. 

With mostly unambiguous data, this protocol has been successfully used for proteins with up to 160 residues [62]. Although virtually all structures converge to the correct fold for small proteins, we observe that approximately one-third of the structures are misfolded for larger proteins, or for low data density, or many ambiguities (see, e.g.. Ref. 63). We have also used this protocol for most structure calculations with the automated NOE assignment method ARIA discussed in the next section. 

Unfortunately, assignment of molecules that are not closely related to the reference molecules becomes a subjective matter of assigning which substituents are similar. The application of the terminology to cases in which the chiral centers are not adjacent is also ambiguous. As a result, the threo-erythro terminology is not a general method of specifying stereochemical relationships. 

In view of the possible ambiguities which can attend conformational assignments based on vicinal coupling constants, it is fortunate that both long-range and geminal couplings each exhibit stereospecific dependences. 

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