| dc.description.abstract | The dimensions of the cis peptide unit obtained as an average from the three sets of data viz., cyclic di-, higher, and tripeptides are summarized in Table 2.11. On a close examination of the Table, the following salient features emerge:
(a) Bond lengths: The bond lengths in general do not show much deviation except C–C, which is 1.51 Å for cyclic dipeptides and 1.53 Å for cyclic higher and tripeptides. The value of 1.53 Å agrees well with that given by Ramachandran and Venkatachalam (1968) and the value 1.51 Å is the same as given by Benedetti (1977) and Kolaskar and Sarathy (1980) (see Table 2.1). It can also be seen from Figs. 2.4a, 2.7a, and 2.9a that there also exists a difference in the peak range values for this bond length (1.50 Å–1.52 Å for cyclic di-, 1.52 Å–1.54 Å for the other two cases). Thus it is clear that there is a distinct shortening of the bond C–C when the cis peptide unit occurs in cyclic dipeptides. The only other bond length which shows some variation is C–N. The variation is only marginal: 1.35 Å for cyclic di-, 1.35 Å for cyclic higher, and 1.34 Å for cyclic tripeptides.
(b) Bond angles: From the values given in Table 2.11, it can be seen that the bond angles show a wider spread than the bond lengths. In particular, the two angles C–CN and CNC? show a marked increase as they occur in cyclic tripeptides as compared to the other two. The mean value of C–CN is 0.5° smaller in cyclic dipeptides and 1.7° higher in cyclic tripeptides when compared to the value 118° in cyclic higher peptides, which is the same as the standard value. The other angles at C, namely, C–CO and OCN do show some variation while the largest value of C–CO occurs in cyclic higher peptides, that of the angle OCN corresponds to cyclic dipeptides. The bond angle CNC? is also noticeably higher in cyclic tripeptides. It is about 3° higher than that in cyclic di- and higher peptides. Regarding the angle CNC? and C?NC?, the former has the same value in cyclic tri- and higher peptides, and is about 2.5° higher in cyclic dipeptides. The angle C?NC?, which is nearly the same in cyclic di- and in higher peptides, is about 2.7° higher than that in cyclic tripeptides. Both at C and N, the increase in the angle C–CN and CNC? in cyclic tripeptides is accompanied by the lowering of the values for the other angles.
From the above it is clear that the cis peptide unit is highly flexible as far as its bond angles are concerned. The internal bond angles C–CN and CNC? either fold in or open out depending upon the geometry of ring closure as well as stereochemical requirements. The case of cyclic tripeptide is particularly interesting, where these two internal angles have opened out by as much as 2°. This is a special need-based requirement in that, in cyclic tripeptides, the intra-annular space has to increase in order that the structure as a whole may be stereochemically favourable. This aspect will be further dealt with in the next chapter.
(c) Planarity at C and N:
Another aspect which can be looked into is the planarity of three bonds meeting at C or N. Quantitatively, the closeness of the sum of the three angles at either of these atoms to 360° is a good indication of the coplanarity of the bonds. The sum of the three angles at C, for all the three cases (cyclic di-, cyclic higher, and cyclic tripeptides) is 359.9° indicating that the bonds are for all practical purposes coplanar. The situation however is different at N atom. The sum is 359.1° for cyclic higher peptides and 359.2° for cyclic tripeptides indicating certain amount of pyramidal nature for N atom in these cases. The sum of the three angles at N for cyclic dipeptides as given in Table 2.11 adds to 361.1°, which is geometrically inadmissible (The maximum in no case can be greater than 360°). This is because the value of 125° for CNC? given in the Table has been obtained by using all the examples, whereas the angles CNC? and C?NC? have been computed using only those compounds which have a substitution at N atom (C?). Hence the pertinent value to be used for checking the planarity at N atom would be the mean of the angles CNC? obtained by taking into account only those examples which have a C? atom. When this is done, the mean value of CNC? turns out to be 123.4° and the sum of the angles at N, 359.7° again indicative of the pyramidal nature of the N atom. The pyramidality however, is a little less pronounced in this case.
It will be interesting to find out the disposition of the bonds at the N atom when the N is not substituted. There are 31 such examples occurring in cyclic dipeptides; and for 14 of these alone H positions have been reported, and using this data the sum of the angles at N when computed shows a spread from 359.6° to 360° with an average of 359.9°. Though this indicates that the bonds meeting at N are more coplanar when there is no substitution, this must be taken with a little caution since in many cases the positions of the H atoms are not as reliable as those of the heavier atoms.
To summarize, the results presented in this chapter indicate that the cis peptide unit has a reasonable degree of flexibility to suit the system in which it occurs. The flexibility in bond angles is more pronounced than that of bond lengths. The dimensions of the unit show a more pronounced variation when it occurs with the amino acid proline. Whether such a flexibility is a general feature of the peptide unit or specific to cis peptide units only can be ascertained by making a similar study on the trans peptide units. However, this has not been attempted, as it falls beyond the scope of the present thesis. | |
