Self-assembled molecules helices

Figure 5.24 Model of hierarchical self-assembly of chiral rodlike monomers.109 (a) Local arrangements (c-f) and corresponding global equilibrium conformations (c -f) for hierarchical selfassembling structures formed in solutions of chiral molecules (a), which have complementary donor and acceptor groups, shown by arrows, via which they interact and align to form tapes (c). Black and the white surfaces of rod (a) are reflected in sides of helical tape (c), which is chosen to curl toward black side (c ). (b) Phase diagram of solution of twisted ribbons that form fibrils. Scaled variables relative helix pitch of isolated ribbons h hh /a. relative side-by-side attraction energy between fibrils eaur/e. Reprinted with permission from Ref. 109. Copyright 2001 by the National Academy of Sciences, U.S.A.

Self-assembly is the spontaneous organization of molecules into stable, well-defined structures with the driving forces being noncovalent associations. The final structure is normally near or at the thermodynamic equilibrium arrangement allowing it to form spontaneously. Such formations can be done under conditions where defects are either minimized or eliminated. In nature, self-assembly is common as in the folding of proteins, formation of the DNA double helix, etc. 

Self-assembly of chiral molecules may result in organized aggregates displaying a remarkable enhancement of ophcal achvity. The best known examples are amino-acid residues that assume a periodic conformation - an a-helix or a p-sheet chain. In this case, the enhancement of optical activity is due to the onset of a parhcular rigid conformation. 

When collagen IV prepared from the EHS tumor is incubated at 37°C, it self-assembles, forming aggregates containing polygonal structures. These lateral associations are stabilized by the interaction between the domain NCI and sites that occur along the triple helix and are separated from one another by about 100 nm (Tsilibary and Charonis, 1986). The additional possibility of lateral aggregation of the molecules would lead to a much more complex three-dimensional structure. 

Helicenes have an intrinsic, rigid helical shape and can be separated into enantiomers. Katz et al. found that the nonracemic helicene 6 with quinone residues self-assembles into one-handed helical columns in apolar solvents, where the molecules are stacked along their helix axes as shown in Fig. 4 [40-42], In this case, the 7r-donor-acceptor interactions appear to induce aggregations and stabilize the columnar stacks. Interestingly, unlike the nonracemic 6, the corresponding racemic 6 produced no such aggregation. 

The emission of Trp 19 in melittin shifts to the red side peaking at 341 nm (Fig. 18), and the probe location slightly moves away from the lipid interface toward the channel center. Consistently, we observed a larger fraction of the ultrafast solvation component (35%) and a smaller contribution of slow ordered-water motion (38%). Melittin consists of 26 amino acid residues (Fig. 9), and the first 20 residues are predominantly hydrophobic, whereas the other 6 near the carboxyl terminus are hydrophilic under physiological conditions. This amphipathic property makes melittin easily bound to membranes, and extensive studies from both experiments [156-161] and MD simulations [162-166] have shown the formation of an 7-helix at the lipid interface. Self-assembly of 7-helical melittin monomers is believed to be important in its lytic activity of membranes [167-169]. Our observed hydration dynamics are consistent with previous studies, which support the view that melittin forms an 7-helix and inserts into the lipid bilayers and leaves the hydrophilic C-terminus protruding into the water channel. The orientational relaxation shows a completely restricted motion of Trp 19, and the anisotropy is constant in 1.5 ns (Fig. 20b), which is consistent with Trp 19 located close to the interface around the headgroups and rigid well-ordered water molecules. 

The use of DNA molecules as wires in electronic systems may open a new opportunity in nanoelectronics. DNA has the appropriate molecular recognition features and well-characterized self-assembly. There is evidence to suggest that DNA is only a marginally better electron conductor than proteins [116-118], As a result, many studies have focused on various methods of DNA modification leading to improvement in its conductive properties. It is possible to enhance the conductivity of DNA by coating it with a thin film of metal atoms, but the molecular recognition properties of the DNA are then destroyed. An effective approach to this problem is the incorporation of metal ions into the DNA double helix [118-121], Preliminary results suggest that a metal ion-DNA complex may be a much better conductor than B-DNA, because the former shows a metallic conduction whereas the latter behaves like a wide-band gap semiconductor [118]. 

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