E and Z Secondary Amides in Supramolecular Nanotubes and Nanospheres - Molecular Self-Assembly: Advances and Applications - page 39

theN-H···OandH···O=Cangles,respectively[41].Deviationfrom
these angles leads to less stable hydrogen bonds. Nevertheless, the
energyprofileresultingfromanglevariations(E f[angles]) is

rather shallow resulting in a somewhat blurred directionality. On
the other hand, elongation of the N···O distance from its ideal 2.9Å
[42] leads to rapid decrease of the hydrogen bond energy which can
reach 5-6 kcal/mol in the best scenarios [43]. It is worth noting
thatthisenergyrisesrapidlythroughacooperativeefectwhen
several amides are interconnected in tape-like arrangements. This
phenomenon resulting from polarization enhancement through

=

σ

and bonds stabilizes the zwitterionic resonance form of amides

within the tape of successive hydrogen bonds. In the process N-H
groups become stronger donors and C=O groups better acceptors
[44,45].

π

2.3 Concepts

Secondary amides that are involved in hydrogen bonds can assume
two geometries: the -amide,

the former being energetically favored over the latter by about 2
kcal/mol[46].Forthisreason,onecansafelyaffirmthatnormal
peptides are almost exclusively composed of

s -trans or E -amide and the s -cis or Z

-amides. On the other
hand,DNAandRNAbaseslikeguanosine,thymidine,anduridine
contain CONH groups related to

E

Z -amides because they are part

of six-membered rings. Both - amides occupy a privileged

position for molecular recognition in biopolymers like proteins and
nucleicacids.For

E - and Z

-amides both the hydrogen bond donor and the
acceptor have opposite directions, whereas they sit side by side and
are parallel in

E

-amides. When several of these important groups
are placed on the edges of small symmetric disk-shaped molecules,
they can develop hydrogen bonding interactions with other similar
molecules(Fig.2.1)[47].

Z

-amide, both the donor and the
acceptor can take part in such intermolecular bonds on opposite
sides of the disc. Consequently, hydrogen bonds will preferentially
be oriented parallel to the

Owing to the geometry of the E

) axis of the disc. The resulting
supramolecules will result in various ways of stacking the discs.
However, the geometry of supramolecules assembled from disks
bearing

C n (or S

n

Z -amidescanbedescribedasendlessflatsheetsbecausethe