Bond conformation

Conformational analysis (Section 3 1) Study of the conforma tions available to a molecule their relative stability and the role they play in defining the properties of the molecule Conformations (Section 3 1) Nonidentical representations of a molecule generated by rotation about single bonds Conformers (Section 3 1) Different conformations of a single molecule... 

Conformation about a Csp —Csp single bond (Conformation of the ring (Nitrogen inversion... 

Glycosyl bond conformation anti anti anti at C, syn at G... 

Among the possible CC bond conformers for 2,2 -dichlorobiphenyl (DCBP) are syn and anti planar structures and two twist structures. 

Coll, M., C. A. Erederick, A. H. J. Wang, and A. Rich. A bifurcated hydrogen-bonded conformation in the D(A-T) base-pairs of the DNA dodecamer D(CGCAAATTTGCG) and its complex with distamycin. Proc. Natl. Acad. Sci. USA 1987, 84, 8385-8389. 

At the opposite extreme, molecular solids contain individual molecules bound together by various combinations of dispersion forces, dipole forces, and hydrogen bonds. Conforming to like dissolves like, molecular solids dissolve readily in solvents with similar types of intermolecular forces. Nonpolar I2, for instance, is soluble in nonpolar liquids such as carbon tetrachloride (CCI4). Many organic compounds are molecular solids that dissolve in organic liquids such as cyclohexane and acetone. 

Fig. 6. Ramachandran plots for simulated Ac-Ala-Xaa-Ala-Ala-NMe peptides with Xaa = glutamine or asparagine, with a constrained side chain-to-backbone hydrogen bond. Conformational distribution for glutamine i (A) and for the residue i +1 to which the glutamine is hydrogen-bonded (B). Conformational distribution for asparagine i (C) and for the residue i +1 to which it is hydrogen-bonded (D).

Cheam, T. C., and S. Krimm. 1990. Ab Initio Force Fields of Alanine Dipeptide in Four Non-Hydrogen Bonded Conformations. J. Mol. Struct. (Theochem) 206, 173-203. 

In the IR-spectra of 4-haloalkyl-3-imidazoline-3-oxides there are two bands Vc=n due to the two conformers A and B (Fig. 2.12) (367, 389). Conformation B corresponds to the form with the lower frequency band Vc=n (Avc=n 30 cm-1), where the halogen atom is located in the plain of the C=N+-0-group in anti -position to the double bond. Conformation A corresponds to the... 

An even stronger case of intramolecular RAHB coupling is provided by the maleate ion (HOOCCH=CHCOO-), whose H-bonded and open conformers are shown in Fig. 5.22. Skeletal bond lengths and bond orders of these conformers are compared in Table 5.18. As shown in Fig. 5.22, the H-bonded conformer is favored in this case by more than 26 kcalmol-1, which is indicative of a powerful intramolecular no aoH interaction (estimated second-order stabilization 104 kcalmol-1) that is sufficient to overcome the severe steric repulsion of the extremely short H- -O nonbonded distance ( 1.3 A).56... 

Experimentally, the cis isomer of DADCE seems to be more stable than the trans isomerl29 Furthermore, in the crystalline state, the cis isomer is known to exist in the hydrogen bonded conformation 130 ... 

By using the arguments presented for dihydroxyethylene, we conclude that the hydrogen bonded conformation will be the preferred conformation for catechol. 

In numerous complex aldol adducts it is not always possible to extract the relevant vicinal proton coupling constants. Heathcock and co-workers have recently noted that for the -hydroxy ketones and esters that exist in the preferred hydrogen-bonded conformations A and A, NMR spectroscopy may be conveniently employed to assign stereochemistry (13). 

This arrangement has reversed the amide bond conformation and thus has... 

Figure 15. The effect of C3-03 bond conformation on the energy profile of 8. Geometries were optimized with the 3-21G basis set. Case I, 03-H bond anti to H3, closed symbols Case II, 03-H bond anti to C4, open symbols.

Some of the complexes were found to exhibit redox potentials that shifted with temperature (230-300 K). The complexes with Cys-Gly-Ala and Cys-Gly-Ala-Cys sequences were found to be particularly susceptible to temperature variations in CH2CI2 (13,14) with positive shifts at (ca. 0.10 V). These shifts were rationalized by the formation of NH—S hydrogen-bonded conformers (see Fig. 5), which are expected to stabilize the reduced forms of the complexes Such a hydrogen-bonded structure has been deduced from the X-ray analysis of several bacterial Fds (26). 

It should be noted, however, that the relative activities of some bicyclic aryloxyethylguanidines do not support this idea that a hydrogen-bonded conformation can bring the aromatic ring and the guanidinium function into the optimum distance. Thus guanoxan (XLVIl) is active, as is the sy -cyclopropyl analogue (XLIX, R = H, = CH2), but the anh-isomer, in which the... 

The presence of intramolecular H bonds in the cross-linked products was probed by carrying out 2-D NMR (NOESY) experiments on cross-linked 26-27, which contains two interstrand intramolecular H bonds. It was found that the same cross-strand NOEs were detected in CDCI3 (Fig. 9.18a) and in H20/THF-r(8 (80/20, v/v Fig. 9.18b). Furthermore, diluting 26-27 from 9 to 0.2 mM in the same aqueous solvent led to no shift in the two aninline NH signals, which remained at 9.75 ppm. These results suggest the persistence of an intramolecular H bonded conformation for 26-27 in aqueous media, which is consistent with the thermodynamic mechanism shown in Figure 9.17. 

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