T-shaped stack

Uracil dimers were studied at the MP2 level using the 6-3IG basis with modified polarization functions. Eleven low-energy minima were located Seven of them are H-bonded, one is T-shaped, and three correspond to various stacked arrangements. The most stable structure was found to be the H-bonded dimer with two Ni-H O2-H bonds (Scheme 85) [98JPC(A)6921]. 

Computational studies on the n-n stacking problem began with the simplest model the benzene dimer. While not the only possible configurations, the benzene dimer structures most studied are the sandwiches 77s (D f) and 77s (T>6 ), the parallel displaced 77pd, and the T-shaped configurations 77t and 77t. ... 

The relative energies of hydrogen bonded versus stacked arrangements of the A-T pair are sensitive to solvent. The stacked monohydrated complex 40 is the fifth lowest energy complex, but for the dihydrated complexes, the stacked form 41 is the most stable. The population of the stacked complexes increases in going from the monohydrated to dihydrated forms. Compared to the G-C pairs, the A-T population is much more favored toward the stacked and T-shaped forms. The preference for the stacked arrangement over the hydrogen-bonded ones in aqueous solution is consistent with experiments. 

Calcified scales formed inside the Golgi and then extruded have so far only been found in coccolithophorids. In other forms, the matrix is formed in the Golgi but calcification takes place in the cytoplasm. In some cases, the plates of coccolithophorids calcify inside the T-shaped cisternae where the stem is associated with the Golgi stack while the scale is already forming with its future distal surface facing the stack. The scales of coccolithophorids always consist of two layers of a cellulose network of microfibrils radially and concentrically arranged. The outer layer of the scale is made up of acidic polysaccharides and small amounts of protein, probably containing hydroxy-... 

The adequacy of the GGA97 set of approximate functionals in describing relative energetics of conformers of a weakly bound intermolecular complex was tested also for the benzene dimer124. The T-shaped conformer was found to be the most stable (Eint =-2.09 kcal/mol). The slipped parallel arrangement was found to be slightly less stable (Ejnj=-1.95 kcal/mol). The stacked conformers were found to be less stable by about 0.5 kcal/mol, whereas the planar conformers were the least stable (Eint = -0.5-0.6 kcal/mol). 

Another issue, closely related to the herringbone-stacking question described in 12.4.2.1, is whether benzene rings show some preferential approach geometry in crystals. Figure 12.12 [27] shows a bimodal distribution with a slight preference for T-shaped couples, but there is also a substantial population of parallel ones and a nonzero population for almost any interplanar angle. 

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