Carbon ground-state geometries

Recently, Hariharan et al. have synthesized and quantified the TT dimer yields of short DNA hairpins with different sequences [13,36]. These small systems are useful tools to probe the exact cause of sequence specificity of TT dimer yields. The three hairpins we will investigate are denoted Stl, St3 and St5 all of which are depicted in Fig. 13.10. Each hairpin has six base pairs that are capped on one end by a twelve carbon C12 linker. The sequences are designed so that each hairpin only has one TT step. The TT step in Stl is on the 5 terminus, in St3 is in the middle of the sequence and in St5 is in the C12 linker adjacent site. Using our molecular dynamics model to compute the TT dimer yields of these sequences will allow us to determine the role of ground state geometry on sequence specificity in TT dimer yields. 

The presence of substituents on the olefinic carbon atoms adds other features to the analysis. Cis isomers can be less stable than trans isomers because of van der Waals repulsion of the cis substituents. This steric interaction can distort the alkene from a perfectly planar ground state geometry, reducing the overlap of the two p orbitals. As a result, photoexcitation of the cis isomer may require shorter wavelength UV-vis radiation than... 

To account for this fact, the TDDFT-B3LYP calculations of the spectra have been carried out with a TZV(2df) basis set augmented with diffuse functions at the sulfur atoms as well as at the neighboring carbon atoms and a TZV(d,p) basis set for the remaining atoms. The B3LYP/TZV(d,p) ground-state geometry has been used for these calculations. The theoretical spectrum has been blue shifted by 0.39 eV to match the experimental band A. 

Compare the geometries of triplet and ground state singlet anthrone. Where do they differ the most Focus on the carbonyl group. Has the CO bond distance altered Does the molecule incorporate a fully-developed CO n bond (as in ground state singlet anthrone), or a single bond (as in phenol) Is the carbonyl carbon planar or puckered Rationalize your observations. 

The ground-state distortion (Table I) from the normal octahedral geometry, i.e., the displacement of the central metal atom by up to 0.34 A toward the oxo from the plane formed by the four cyano carbon atoms, is in further agreement with this reasoning, indicative of more reactive complex with an increased metal-oxygen bond length. 

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