Stacking structure

MP2/6-31G calculations were performed for bonded and stacked structures of adenine-2,4-difluorotoluene complexes 152 [99CPL393] and for adenine with guanine or thymine [97JPC(B)3846]. Classical base pair structures of 152... 

The result is explained by considering the stacking structure between the quinoline moiety and the benzene ring linked to the carboxylic acid, which gives the cavity size adequate for Li+. (Fig. 3) Several selective host molecules for Li+ such as [13]crown-4 18), [14]crown-4 19), [16]crown-4 20>, or noncyclic polyether amide derivatives 21) also possess trimethylene moiety, and this is an interesting finding from the point of view of molecular design of new host molecules for Li+. 

An alternative possibility is a vertical stacking structure where the p-strands are arranged on top of each other, again satisfying electrostatic and hydrophobic packing considerations (Fig. 20). Whichever is more likely, this is still far from a complete picture because the exact arrangement of the two disulphide-linked peptide chains is not yet known. 

In addition to the spreading dynamics, the stacking structure of the self-spreading lipid bilayer is also controllable via the NaCl concentration [54, 55]. Further experimental and theoretical investigations regarding the control of self-spreading are required before we will be able to easily control the self-spreading behavior in microfluidic devices. 

When the donor group is attached at a /3-pyrrole position rather than the meso position, the properties of the assemblies change. Knapp (57) synthesized a series of /3-pyrrole 2-pyridyl substituted zinc porphyrins (49, Fig. 16) and showed that dimerization takes place provided the meso-substituents are not too bulky H NMR and VPO measurements showed that the porphyrin, which bears heptyl substituents, dimerizes in solution, whereas the phenyl analog does not. The complexation-induced changes in chemical shift suggest a stacked structure for the dimer. 

Polyphosphazene-Phthalocyanlne Structures. Thus, a related study was carried out with copper phthalocyanine units linked covalently to a poly(aryloxyphosphazene) (44). Non-polymeric copper phthalocyanine forms ordered stacked structures in the crystalline state. When... 

The innate sensitivity of DNA-mediated CT to perturbations in the TT-stack has prompted us to employ this chemistry as a probe of stacking structure and dynamics. We have developed a new class of DNA-based diagnostic tools that diagnose DNA mutations such as single base-pair mismatches and lesions, analyze DNA-protein interactions, and probe the sequence-depen-dent dynamics and flexibility of DNA. These applications rely on electrochemical probing of CT in DNA films self-assembled on gold electrodes. 

The analogy drawn between -stacked solids and duplex DNA has provided a useful starting point for experiments to probe and understand DNA-medi-ated CT. As with the -stacked solids, the DNA base pair array can provide an effective medium for long range CT. Mechanistically, however, the differences between DNA and these solid state materials may be even more important to consider. Duplex DNA, as a molecular -stacked structure, undergoes dynamical motion in solution. The time-dependent and sequence-dependent structures that arise serve to modulate and gate CT. Indeed in probing DNA CT as a function of sequence and sequence-dependent structure, we may better understand mechanistically how CT proceeds and how DNA CT may be utilized. 

The g-tensor principal values of radical cations were shown to be sensitive to the presence or absence of dimer- and multimer-stacked structures (Petrenko et al. 2005). If face-to-face dimer structures occur (see Scheme 9.7), then a large change occurs in the gyy component compared to the monomer structure. DFT calculations confirm this behavior and permitted an interpretation of the EPR measurements of the principal g-tensor components of the chlorophyll dimers with stacked structures like the P 00 special dimer pair cation radical and the P700 special dimer pair triplet radical in photosystem I. Thus dimers that occur for radical cations can be deduced by monitoring the gyy component. 

D Intensity. As already mentioned (cf. p. 126 and Fig. 8.12), the isotropic scattering of a layer-stack structure is easily desmeared from the random orientation of its entities by Lorentz correction (Eq. 8.44). For materials with microfibrillar structure this is more difficult. Fortunately microfibrils are, in general, found in highly oriented fiber materials where they are oriented in fiber direction. In this case the one-dimensional intensity in fiber direction,... 

Fig. 4 Schematic drawing showing the [5-form MnPc stacking structures a and the ionic radii of the metals b. Figure obtained from [39]...

Generally, the ionization of Pcs not only increases their solubility but also alters their %-% stacking structures, especially in the presence of large balanced ions. The Pc skeleton in these compounds can be integrally or partly oxidized cationic H2Pc+, or anionic Pc(l-) and Pc(l-). According to the charge type of Pc moiety, ionic Pcs can be classified as cationic Pcs and anionic Pcs. The cationic and anionic Pcs published recently are listed in Tables 7 and 8, respectively. 

However at elevated temperatures (T2 > Tj, Figure 9) the increased entropy (TAS) associated with an open shell structure overcomes the ti —ti enthalpy of dimerisation associated with these distorted Ti-stacked structures and they undergo a solid-solid phase transition (Figure 9) The high temperature phase is typically associated with a Ti-stack of regularly spaced radicals which exhibit longer inter-radical S- S contacts (ca. 3.7 A). This process was first observed by Oakley60 in the DTA radical thiadiazolopyrazine-l,3,2-dithiazolyl 26, and a number of other derivatives have subsequently been identified which exhibit similar behaviour. These are compiled in Table 1. 

Only 5 derivatives have been isolated to date. While the non-fused system forms a 71 -ji dimer (<7S s 3.27 A),86 structural studies on the more delocalised derivatives indicate a reduced tendency to dimerise. However, rather than forming optimal n-stacked motifs, there is a clear tendency to adopt slipped n-stack structures which minimise orbital overlap. As a consequence although the Hubbard energy is low, conductivity measurements show poor conductivities (10 5 S cm-1) similar to those observed in either the isomeric 1,3,2-dithiazolyl (4) or 1,2,3,4-dithiadiazolylradicals (2).84... 

Fig. 8 Local transmission pictures in a superposed benzenoid structure. As the two rings change geometry from an eclipsed pseudo para geometry (upper left) through an eclipsed pseudo meta geometry to a slip-stacked structure to a single tunneling pathway, the transmission at the Fermi energy increases hy roughly a factor of ten. Reprinted with permission from G. C. Solomon et al. J. Am. Chem. Soc. (2010) 132, 7887-7889. Copyright 2011 American Chemical Society...

As discussed in section 2.2, a mixture of AMP and AA showed two solid condensed phases above and below about 30 mN m- [5,10]. A loosely stacked structure of two porphyrins was proposed for LB films prepared at higher surface pressures than 30 mNmr1, which was caused by squeezing-out of a monomolecular structure formed at lower surface pressure [5,10]. In this section, photoelectric characteristics of LB films containing AMP and AA deposited at two solid condensed phases will be discussed in relation to multilayer structure and the anisotropic intermolecular tunneling rates [87]. Seven monolayers of 1 5 or 1 10 mixture of AMP and AA were deposited at 20 and 50 mN m-1 on an ITO plate at 18 °C to form stable Y-type LB films. Aluminum was vacuum evaporated onto LB films as sandwich-type electrodes at 10-6 Torr. Steady photocurrents were measured in a similar manner as mentioned above. 

OLED devices are fabricated on a glass, plastic, metal, or ceramic substrate as a multilayer-stacked structure represented in Figure 3.1. 

Fig. 2. Stacking model.69 Phenyl rings form the regular stacking structure between L and D molecules. Bold lines show the a-helical axes. Reproduced with permissions from Elsevier Science.

The riL value of racemic PBG-ytL is several hundred ms and decreases gradually as temperature increases. These results show that the side chains participating in the stacking structure are not rigid. Tx at the y position below room temperature is governed by the rapid and small-amplitude libration as shown in Section 4.3. The libration is expected to exist in the stacked state as well as the free state. riL is considered to be governed by libration in the stacked state. In order to estimate the amplitude of the libration in the stacked state, we extracted the Tu component of the spectrum in the same way as that used for racemic PBG- d2. The spectra of the T1L and T, s components are shown in Fig. 37. The vq value of the r1L component is... 

The amplitude and correlation time rc of the libration in the stacked state are estimated by using the diffusion in a cone model. The semiangles of the cone 6C are obtained to be 17°, 18°, and 19° for the riL component at 20, 40, and 60°C, respectively, while 20°, 22°, and 22° for the PBLG-yd2 at 23, 40, and, 55°C, respectively. The 6C in the stacking structure is smaller by 3° to 4° than that in the free state at the y position. Comparing the 6C value at the y position with that at the position in the stacked state, the 6C value at the y position is 5° smaller than that at the position at 20° C. This is because the Cf 2H bond is located at a more terminal part of the side chain than is the Cy 2H bond. The rc values were obtained to be about 10 11 s for both stacked and free states in this temperature range. There is little difference in the correlation time between the stacked and free states. 

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