Self-complementary

Amino-5 -deoxy-2, 3 -0-isopropylideneadenosine was acylated at N-5 with an activated derivative of the 6-carboxy-2-naphthyl ester of Kemp s acid imide. The resulting molecule possesses self-complementary binding sites, the key feature of replicating molecules that act as templates for their own reproduction. The dimer of this molecule is, however, not very stable K = 630 L mol ). When the two initially mentioned educts are added, a small proportion of the ternary complex is also formed and undergoes a fast, template-catalysed... 

Fig. 31. Supramolecular (hydrogen-bonded) motifs of self-complementary molecules (196).

FIGURE 12.27 The formation of a cruciform structure from a paliudromic sequence within DNA. The self-complementary Inverted repeats can rearrange to form hydrogen-bonded cruciform loops. 

To conclude this section, we note quickly a few other asymptotic enumerations. In [PalE70] Palmer found an asymptotic estimate for the number of self-complementary graphs and digraphs. Robinson [RobR76] and Stanley [StaR73] enumerated acyclic digraphs, and obtained the asymptotic estimate... 

OttR48 Otter, R. The number of trees. Ann. Math. 49 (1948) 583. PalE70 Palmer, E. M Asymptotic formulas for the number of self-complementary graphs and digraphs. Mathematika 17... 

PalE77 Palmer, E. M., Schwenk, A. J. The number of self-complementary achiral necklaces. J. Graph Theory 1... 

ReaR63 Read, R. C. On the number of self-complementary graphs and digraphs. J. London Math. Soc. 38 (1963) 99-104. ReaR68 Read, R. C. The use of -functions in combinatorial analysis. Canad. J. Math. 20 (1968) 808-841. 

WilD78 Wille, D. Enumeration of self-complementary structures. J. Comb. Theory B 25 (1978) 143-150. 

Zhang SG, Holmes T, Lockshin C et al (1993) Spontaneous assembly of a self- complementary oligopeptide to form a stable macroscopic membrane. Proc Natl Acad Sci 90 3334—3338... 

When the metalloporphyrin bears a donor group on its periphery, it can behave as a self-complementary ditopic unit capable of metal-ligand induced dimerization. Many systems have been synthesized using different metals, ligands, and spacers. The length and geometry of the spacer groups determine the stoichiometry of the assembly process. 

Both theoretical and experimental data (in the solid, liquid, and gas phases) prove that the tendency of halocarbons to work as XB donors decreases in the order I > Br > Cl [66-68]. Clearly, polarizability and not electronegativity plays a key role. 3-Halo-cyanoacetylene works as self-complementary module and the N X distance is beautifully consistent with the scale reported above, being 2.932, 2.978 and 2.984 A in the iodo, bromo and chloro derivatives, respectively [69,70]. The same trend is observed when a phenyl, rather than a triple bond, spaces the donor and acceptor sites. The N Br distance in 4-bromobenzonitrile is longer than in the 4-iodo derivative [71,72] and no XB is present in the chloro and fluoro analogues, wherein molecules are pinned by N H and X- H short contacts [73]. PFCs have a very poor tendency, if any, to work as XB donors [74-77] and no crystal engineering can be based on such tectons. However, F2 is a quite strong XB donor and several adducts have been described in the gas phase [11,18] (see also the chapter by Legon in this volume). 

When both the donor and the acceptor modules are bidentate, infinite chain (ID polymers) are formed. The simplest case is when the axes of the donor and acceptor sites are parallel and coaxial so that linear polymers are formed. This is the case in the homopolymers formed by bidentate and self-complementary tectons (e.g. 4-iodopyridine [157], 4-iodobenzonitrile [71, 72], halocyanoacetylenes [70]) and in the co-polymers formed when dihalo-carbons interact with dinitrogen, or dioxygen, substituted hydrocarbons (e.g. the systems formed when 1,4-DITFB, or 1,4-DIB, interact with 4,4/-BPY [50], when 1,4-dinitrobenzene interacts with 1,4-DIB [ 158-162]J, and when 1,4-DITFB interacts with DABCO [163]) (Fig. 7). 

Fig. 7 Linear ID infinite chains formed on self-assembly of bidentate and self-complementary modules where donor and acceptor sites axes are parallel and coaxial (A), of bidentate donor and acceptor modules where donor and acceptor sites axes are parallel and coaxial (B), or are parallel and translated from each other in the XB donor (C) or acceptor (D) module, respectively...

From a topological point of view, the homocrystal of l,3-di(4-pyridyl)-2,4-di(4-iodiotetrafluorophenyl)cyclobutane, which is a self-complementary and tetradentate module, also presents a (4,4) net [176]. 

Fig. 14 Different adamantanoid architectures formed on self-assembly of A a self-complementary tetradentate module B a tetradentate XB acceptor and a bidentate XB donor C a tetradentate XB acceptor and a tetradentate XB donor...

Kind R (2007) Evidence for Ferroelectric Nudeation Centres in the Pseudo-spin Glass System Rbi x(ND4)xD2P04 A 87Rb NMR Study. 124 119-147 Klapotke TM (2007) New Nitrogen-Rich High Explosives. 125 85-121 Kobuke Y (2006) Porphyrin Supramolecules by Self-Complementary Coordination 121 ... 

It has also been noted that self-complementary objects must follow twofold sym-... 

In spite of all these successes, critics point out that from the perspective of biogenesis and the self-replication methods reported, nature uses matrices which are almost solely complementary, and not self-complementary. These concerns also include Orgel s result that a C-rich oligonucleotide leads, after replication, to a G-rich polymer which itself has only very limited use as a matrix. All these results refer to experiments on mononucleotides, so that the question arises as to whether the behaviour previously observed would remain unchanged if oligonucleotides were used instead of monomers. 

We still need to clear up one or two points of nomenclature in normal replication of nucleic acids, the matrix (the + strand) and the newly formed daughter strand (- strand) are held together by Watson-Crick hydrogen bonding. This process is also referred to as cross-catalytic . Normal autocatalysis is different it leads to a product which corresponds in structure to the matrix, so that there is no difference between the + and - strands. Such self-complementary sequences are called palindromes. 

A recent discovery that RNA will act as a self-catalyst, called a ribozyme, leads to a simple three-step model for self-replication - this might include a surface. In the model (Figure 8.18), the template molecule T is self-complementary and is able to act as an autocatalyst. In the first step, it reversibly binds with its constituents A and B, forming the termolecular complex M. The termolecular complex undergoes irreversible polymerisation and becomes the duplex molecule D. Reversible dissociation of D gives two template molecules T, which can initiate new replication. The model preserves the order of the moieties on the template (the direction of the arrow) and the backbone, which may be on the surface... 

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