Stacking interactions, determination

Combined quantum mechanics/molecular mechanics studies have demonstrated that 7r-7r stacking interactions are important in determining the structural features of polyarene transition metal compounds such as the two ds Pd complexes.96... 

The nature of the interaction between a ligand and its receptor or a substrate and its transporter is strongly determined by the local environment (or solvent) in which the molecular encounter takes place. If the encounter takes place in an aqueous environment (with a dielectric constant, e s 80), then hydrophobic, van der Waals, or stacking interactions are predominant. Electrostatic interactions are also possible. 

Most of the reported X-ray studies have been carried out to establish structures or conformations of different compounds. The X-ray of fully conjugated diene compound 20 has been reported showing supramolecular assemblies resulting in a 7i-stacking interaction between two adjacent molecules <2004TL7363>. The other structures reported in Figure 2 have been determined and parameters described in the corresponding papers. 

Complexation experiments show that compounds of type 2 are good receptors for dihydroxybenzenes, as expected [11]. Two types of interaction-hydrogen bonding and n-n stacking interactions - cooperate to bind a guest molecule in the cleft of the clip. Association constants for 3 and 5-7 with dihydroxy-substituted aromatic compounds were determined using H-NMR titrations in CHCI3 (Table 1). The role of n-n interactions is evident from the difference in... 

Figure 1. Catalysis and template action of RNA and proteins. Catalytic action of one RNA molecule on another one is shown in the simplest case, the "hammerhead ribozyme." The substrate is a tridecanucleotide forming two double-helical stacks together with the ribozyme (n = 34) in the confolded complex. Tertiary interactions determine the detailed structure of the hammerhead ribozyme complex and are important for the enzymatic reaction cleaving one of the two linkages between the two stacks. Substrate specificity of ribozyme catalysis is caused by secondary structure in the cofolded complex between substrate and catalyst. Autocatalytic replication of oligonucleotide and nucleic acid is based on G = C and A = U complementarity in the hydrogen bonded complexes of nucleotides forming a Watson-Crick type double helix. Gunter von Kiedrowski s experi-...

Since the IR spectrum of an RNA molecule has numerous features, IR spectroscopy is not limited to the determination of the fraction folded only. Depending upon the wavenumber of the transition, IR spectroscopy can distinguish A-U base pairs from G-C base pairs as well as the more complex base pairing schemes found in triple helices (Banyay et al., 2003 Brauns and Dyer, 2005). Similarly, base stacking interactions can be distinguished from base pairing interactions. It has even been shown that transfer RNAs of different species can be distinguished from their IR spectra (Thomas, 1969). 

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