Dimeric model system

Reagents and conditions (i) Ni(dppp)Cl2, ether, reflux (ii) NBS, CHClg-acetic acid, RT (iii) TMS-acetylene, Pd(PPh3)4, Cul, EtgN, 80 °C (iv) KOH, benzene-MeOH, RT (v) Cu(OAc)2, pyridine, 45 °C (vi) Na2S.9H20, KOH, dioxane, reflux. 

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Figure 15.2 Helical wheel and sequence representation of the antiparallel, dimeric model system. The substitution positions are highlighted in one strand with an open square for the hydrophobic core and an open circle for the charged domain. Their direct interaction partners in the opposite strand are shaded in gray squares or circles, respectively. The ligation site is marked with an arrow.

Figure 15.8 Helical wheel and sequence representation of the parallel, dimeric model system. The substitution positions are highlighted in gray. Their main interaction partners are encircled in black.

Figure 1 Planar water dimer model system. The dipole angle (measured from the horizontal) is labeled as 0.

Ab initio molecular orbital calculations for the model systems RCN3S2 (R = H, NH2) show that these dithiatriazines are predicted to be ground state singlets with low-lying triplet excited states (Section 4.4). The singlet state is stabilized by a Jahn-Teller distortion from C2v to Cj symmetry. In this context the observed dimerization of these antiaromatic (eight r-electron) systems is readily understood. 

The dimer model proposed by Wilson [83] was found not to exhibit a nematic phase but smectic A and B phases and so, although semi-realistic features are included, the model is not able to reproduce the behaviour of real dimers such as the a,co-bis(4 -cyanobiphenyl-4-yloxy) [87], which exhibit nematic phases, although liquid crystal dimers exhibiting smectic phases are also known [88]. In these simulations, the GB-GB interaction appears to be too strong and so the system forms a smectic phase in which the GB and LJ units... 

In order to investigate the single electron donation process from a reduced flavin to a pyrimidine dimer or oxetane lesion, the photolyase model compounds 1-4 depicted in Scheme 4 were prepared [41, 42]. The first model compounds 1 and 2 contain a cyclobutane uracil (1) or thymine (2) dimer covalently connected to a flavin, which is the active electron donating subunit in photolyases. These model systems were dissolved in various solvents... 

These experiments proved that a light-excited, reduced flavin is indeed able to photoreduce cyclobutane pyrimidine dimers and that these dimers undergo a spontaneous cycloreversion. The quantum yield of about 0=5% clarified that the overall dimer splitting process is highly efficient, even in these simple model systems ((]) photolyase 70%). 

The theory had never been tested on a logical model system. Let us consider in detail one representative case, the superimposable stacking of the two benzene rings, one from each triplet diphenylcarbene molecule. These are considered to represent idealized modes of dimeric interaction of the aromatic ring parts of open-shell molecules in ordered molecular assemblies like crystals, liquid crystals and membranes. 

The results of EPR studies of photoezcited triplets of model systems show that it is not possible to give generally applicable rules for the interpretation of the spectroscopic data. In a number of cases there appears to be a well-understood relationship between dimerization effects and dimer geometry. In most of the systems considered here that is not the case. It is not clear to what difference in make-up of the dimers this discrepancy must be attributed and this is an interesting point of further investigation. Evidently, as long as the data on fairly well characterized model systems are not fully understood it will be impossible to derive definitive conclusions concerning the structure of the special pair from data on its photoexcited triplet state. 

The mechanism of dimer cleavage has been probed in model systems, including bifunctional ones in which a sensitizer (e.g., indole) is linked to the pyrimidine dimer. Work on a linked dimer (64), suggested that a dimer radical cation is a discrete (short-lived) minimum. ... 

Bryce and Wasylishen196 have presented ab initio calculations of 2hJ(N, N) couplings using a MCSCF wave function taking the methyleneimine dimer [8] as a model system. 

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