T-stacking

Figure 25 Rings and chains of T-stacking of CTeI2 moieties...

Solid State Properties. Most likely as a result of the limited intermoleeular interactions of these complexes in the solid state, little investigation of their solid-state properties have been reported. However, the electrical conductivity of pressed pellets of 17 have been measured via four-point probe to give a room temperature value of 10 S cm. This relatively low value is likely a result of the lack of significantly strong t-stacking as observed in the X-ray structure. 

The early studies of Risser, Beratan, and Meade [13] suggested that, at short distances (especially for backbone-tethered donor-acceptor pairs), backbone mediation could dominate the coupling interactions. Later studies by Priyadarshy, Tong, Kurnikov, Risser, and Beratan showed that—for t-stacked donor-acceptor pairs—base interactions clearly dominate the bridge-mediated coupling interactions [12,16]. 

Thermal fluctuations are known to affect considerably the structure and other properties of biomolecules [30]. Recently, it was recognized that conformational changes in DNA can produce significant variations in the t-stacking of base pairs and thereby modulate the efficiency of charge transfer [31-33]. Thus, one has to employ a combination of molecular dynamics... 

The electronic coupling of donor and acceptor sites, connected via a t-stack, can either be treated by carrying out a calculation on the complete system or by employing a divide-and-conquer (DC) strategy. With the Hartree-Fock (HF) method or a method based on density functional theory (DFT), full treatment of a d-a system is feasible for relatively small systems. Whereas such calculations can be performed for models consisting of up to about ten WCPs, they are essentially inaccessible even for dimers when one attempts to combine them with MD simulations. Semiempirical quantum chemical methods require considerably less effort than HF or DFT methods also, one can afford application to larger models. However, standard semiempirical methods, e.g., AMI or PM3, considerably underestimate the electronic couplings between r-stacked donor and acceptor sites and, therefore, a special parameterization has to be invoked (see below). 

In addition, models will need to change when an intercalated or bound chromophore is taken into account. Two issues should be considered in this context structural changes of the DNA fragment due to its interaction with chromophore and photochemical hole injection into the t-stack. 

T-stacking and charge-transfer interaction between aromatic residues in the... 

L313F surface, helix 8, active site cleft 5 T stacks with Phe314. 

Where does this aU leave us concerning ji-stacking Iverson argues that the term is loaded with context that no longer has any value. He suggests that t-stacking and jc-jc interactions are terms that are misleading and should be avoided. The computational results discussed here certainly point toward that confusion. 

Weakly polar interactions in proteins and protein-ligand complexes are frequently phenomenologically analyzed and classified in terms of the interacting partners (36). This especially includes interactions with x-sys-tems, such as the NH-T, OH-T, or CH-ir interaction (37, 38), aromatic-aromatic interactions (parallel t-t stacking versus edge-to-face interaction), and the cation-T interaction (39). All of these can mostly be rationalized in terms of electrostatic interactions outlined above that is, they involve interactions between monopoles, dipoles, and quadrupoles (permanent and induced). A more distinct character can be attributed to metal complex-ation, which can play a significant role in individual cases of protein-ligand interactions, as for example in metalloenzymes (2,40, 41). 

However, on addition of Cu(OTf)2 to the solution, the resulting suspension showed strong CD bands.219 Because no gelling effect was observed and the absorption position did not change on addition of Cu(OTf)2, the CD bands which appeared due to the effect of Cu2+ are not based on the "T-stacked aggregate suggested for 126—128 but on a helical conformation of a single molecule induced by the complexation with Cu2+. 

Lipkowitz K. B., D Hue C. A., Sakamoto T, Stack J., Stereo-cartography A Computational Mapping Technique That Can Locate Regions of Maximum Stereo induction around Chiral Catalysts,/. Am. Chem. Soc. 2002, 324, 14255-14267. 

The voltage data of Fig. 6.4 are presented also in terms of stack efficiency curve in Fig. 6.6, where t/stack is plotted against the electric power produced by the FCS and measured at the DC-DC converter inlet. In the same hgure, the actual and theoretical curves of FCS efficiency (j/fcs) are also reported, they refer to the real consumptions of ancillary components or to the ideal losses expected for that same system after optimization of all individual components (maximum FCS efficiency in Fig. 6.6). The stack efficiency varies from 0.7 at 0.1 kW to 0.56 at... 

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