Conformational populations

CONFORMATIONAL POPULATION INCREMENT (POP) TORSIONAL CONTRIBUTION (TOR) TRANSLATION/ROTATION TERM (T/R)... 

Process structures with appropriate quantum or molecular mechanical technique to compute desired properties eg, relative energies, dipole moment, conformer populations, size, shape, etc. 

We noted in Section 13.13 that an NMR spectrum is an average spectrum of the conformations populated by a molecule. From the following data, estimate the percentages of axial and equatorial bromine present in bromocyclohexane. 

Another interesting question concerns the rate at which each tosylate undergoes elimination. A tosylate sample contains molecules with several different conformations. The size of each conformer population depends on conformer energy, and the more reactive tosylate will probably be the one with the largest population of reactive conformers, i.e., molecules whose geometries allow anti elimination. Which tosylate, cis or trans, will have a larger population of reactive conformers Explain how you reached this conclusion. 

Conformational populations of cyanomethylphosphine oxides (136) have been estimated from dipole moments and indicate a preference for the tra/15-conformation. The moments of the o-, m- and p-chloro- and tolyl-derivatives of triaryl phosphites (137, Y = ) and triaryl phosphates (137 Y = O) indicate that the oxygen atom in the latter series causes the aryl rings to rotate further away from a position in which their planes all meet along the molecular symmetry axis. Conformational studies have also been carried out on the dioxaphosphorinanes. The moments of the isomeric series (138a) and (138b) were in the ranges 3.7—4.2 and 5.4—5.5 D respectively. ... 

Using this procedure, the classic RIS model for the atomistic chain has been adapted so that it influences the conformations populated by the coarsegrained chain on the high coordination lattice. 

Cifra, P. and Bleha, T. Conformer populations and the excluded volume effect in lattice simulations of flexible chains in solutions, Polymer, 34 (1993). 3716-3722... 

The tetraantennary oligosaccharide illustrated in Figure 14.2 has been shown to present an umbrellalike structure as one of the major conformational populations.14,15 The distance between terminal sugar residues interacting with receptors may vary from 8 to 30 A. In the case of the phosphorylated high-mannose ligands for the MPR, the distance between phosphates is 15 A.16... 

Figure 14.3 Structure models of four different conformer populations (2 for each 1—>6 link) of a triantennary high-mannose undecasaccharide M9. Terminal mannoses are highlighted as CPK models.12...

Examining the CD spectra of the newly prepared (see Table 4) thiocyclo-hexanones (for one example, see Figure 8) and making the assumptions that (i) the conformer population is not affected by the nature of the solvent, (ii) the... 

The acid-catalyzed ester hydrolysis provides a good target for MM treatments. DeTar first used hydrocarbon models in which an ester was approximated by an isoalkane (74) and the intermediate (75) by a neoalkane (76). He assumed that if the rate of reaction truly is not influenced by polar effects but is governed only by steric effects of R, as has been generally postulated, the rate must be proportional to the energy difference (AAH ) between 74 and 76. The AAH f is mainly determined by the van der Waals strain in these branched alkanes. Nonsteric group increment terms were carefully adjusted, and statistical mechanical corrections for conformer populations... 

With three linkage bonds as in the molecular mechanics study of the 1-6 disaccharide gentiobiose (12), the lowest 24 minima within 7 kcal mole which were reported did not include that observed in the crystal structure (20). Had the crystal structure conformation been one of the sets of starting parameters, it would have been included, but it is reasonable to assume that the conformational population in solution was also not fully represented. 

Conformer populations were calculated on the basis of the following relationship ... 

Table II. Calculated Energies and Conformation Populations of -Dimethylxylaraiiiide (1) Using UacrcModel V 2 ...

When a van der Waals cutoff radius of 3 A was used to calculate the conformational populations of JV,J -dihexylxYlaramide (2), similar results were obtained (Table III). Sickles-1 and 3 and the Extended conformation accounted for 94% of the total conformational population. Again, good agreement was obtained for calcd (3.66 Hz) and J2 3 xpt (3.32 Hz). 

Table I. Qualitative Conformer Populations of idoA and Sulfated idoA (idoAg) in Different Compounds (+ Corresponds to about 20%)...

These conformer populations were confirmed by a number of n.O.e. measurements (the H2—H5 distance can act as a marker in identifying the ring form). The case of a hexasaccharide (compound 23 in Ref. 9) where the three IdoA residues yield different n.O.e. enhancements, is striking. Moreover, models computed with molecular mechanics have been put forward for the peculiar pentasaccharide of heparin. The models are in acceptable agreement with the observed vicinal coupling constants and n.O.e. values (10) (a full paper by Ragazzi, M. et al. Carbohvdr. Res.. is in press). 

Table 2. Minimum energy conformations and conformer populations for a series of glucos-phyngolipids and glucoglycerolipids. Values are obtained by MM3 minimizations at a value of dielectric constant e=4 [ 151 ] 9 V ei ...

---