Space-filling models, substituted

Figure 14.2 Models of a collagen-like peptide with a mutation Gly to Ala in the middle of the peptide (orange). Each polypeptide chain is folded into a polyproline type II helix and three chains form a superhelix similar to part of the collagen molecule. The alanine side chain is accommodated inside the superhelix causing a slight change in the twist of the individual chains, (a) Space-filling model, (b) Ribbon diagram. Compare with Figure 14.1c for the change caused by the alanine substitution. (Adapted from J. Bella et al.. Science 266 75-81, 1994.)...

Next, examine the Sn2 transition states as space-filling models. Are you able to identify unfavorable nonbondec (steric) interactions that are not present in the reactants If so, which Sn2 reaction is likely to be most affected b] steric interactions Least affected Rationalize you observations. Hint Compare CBr bond distances in thf Sn2 transition states. How do these change with increasec substitution at carbon What effect, if any, does this havf on crowding ... 

Trans isomers of 1,2-dialkyl-substituted ethenes evolve less heat (are more stable) than the corresponding cis isomers. This is the result of molecular overcrowding in the cis isomers from nonbonded interactions between two alkyl groups on the same side of the double bond. The effect amounts to almost 10 kcal mole-1 with two cis-tert-butyl groups. This effect is another manifestation of steric hindrance and can be seen most clearly with space-filling models (Figure 11-3). 

Exercise 12-24 Space-filling models (Section 2-2B) indicate that the chiral forms of frans-cyclopentadecene are likely to be readily interconverted at room temperature. How and where might frans-cyclopentadecene be substituted to give stable chiral forms that possess a chiral center but no chiral carbon atoms ... 

Fig. 19 Main plot SAXS intensity (I) vs momentum transfer for a solution of 51 in acetonitrile (5.1 g L 1). The symbols and the solid line correspond to the experimental data points and the numerical fit using GNOM/DAMMIN simulated annealing, constraining the symmetry to the point group P432 (% = 1.397). Inset reconstructed low resolution particle shape for 51 obtained by the GNOM/DAMMIN fit (semitransparent spheres) superimposed onto the PM3 stationary point (space-filling model, iso-butyl groups substituted by methyl groups)...

Figure 100. Structures of cyano-substituted oligo(m phenylene ethynylene)s and a space filling model of 54 coordinated to two Ag+ ions. Side chains have been omitted for clarity.

This relationship was of interest for several reasons. Firstly it indicated that the biological assay was sufficiently precise to enable the QSAR approach to be used Secondly the observation that only 2dkyl substituents R affected the activity whereas alkyl substituents in the R position apparently had little influence. This parallels the observations in the 6-thioxanthine series where a similar relationship was derived for the bronchodilating activity ( ) Thirdly, bulky substituents in the Rp position had a beneficial effect. Benzyl-substituted conqiounds e.g. (v) were more active than equation 1 indicated, possibly because the usual value of Es for benzyl did not reflect the buttressing effect of the adjacent triazole ring as revealed by a study of space-filling models ( ). 

Fig. 4 Representative membrane-active peptides that have been studied by solid-state 19F-NMR. (a) The primary sequences show which positions were substituted (filled green boxes) or which ones could in principle be substituted (dotted green lines), (b) Characteristic conformations of the peptides in the membrane-bound state. The space-filling solvent-accessibility models emphasize the amphiphilicity by colouring hydrophobic residues in yellow and cationic side-chains in blue. (c) Observed structures and alignment states of the peptides as determined by 19F-NMR...

The construction of computer and CPK space-filling molecular models is based on established physical and chemical parameters. While models cannot substitute for direct experimental evidence, they can be used to describe rather successfully structures of biochemicals, molecular interactions, reaction products and many aspects of molecular d)mamics. Models may be particularly helpful in depicting the chemistry of active sites of enzymes, antibodies and receptors. Accordingly, the interaction of models described... 

These observations have led to the construction of a simple model which allows one to predict the diastereoselectivity (i.e., the syn/anfi-ratio) of yeast-catalyzed reductions of cx-substituted p-ketoesters (Fig. 2.17) [903]. Thus, when cx-substitu-ents are smaller than the carboxylate moiety, they fit well into the small pocket (S), with L being the carboxylate, but substrates bearing space-filling groups on the... 

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