Linking the atomistic scale and the mesoscale: molecular orbital and solid state packing calculations on poly(p-phenylene)

The energies and structures of neutral benzenoid and neutral quinonoid polyphenylenes in the gas phase were calculated at the ab initio and semi-empirical levels for oligomers containing up to 11 rings as a function of the torsion angles between consecutive aromatic rings. In the gas-phase poly(p-phenylene) (PPP) simulations, a transition to the aromatic benzenoid structure occurs in the centre of chains as short as about six to seven rings. The development of electronic properties such as ionisation potential, the carbon-carbon bond length between rings, the band gap and width of the highest occupied bands were studied. On going from a coplanar to a perpendicular conformation, qualitatively, the ionisation potential and band gap values increase and the band widths of the highest occupied bands decrease. Molecular mechanics simulations were used to model the crystal structures of PPP oligomers using Lennard-Jones and sinusoidal torsion potentials, with parameters derived initially from the gas-phase calculations. These solid state simulations reproduced known crystal structures and predictions are made for the crystal structures of PPP oligomers up to a degree of polymerisation of 11. The crystal packing forces the PPP molecules to be planar, hence increasing conductivity in the solid state. Interestingly, there is an anomaly in the packing energy results for the sexiphenylene case which is in accord with the gas phase calculations.     

The "clustered structure" of the purines/pyrimidines distribution in DNA distinguishes systematically between coding and non-coding sequences

A method allowing to measure the inhomogeneous distribution of purines/pyrimidines in nucleotide sequences is developed. We show that this measure relates to the coding or non-coding character of the considered sequence. Coding sequences present a near to the random Pu or Py distribution. This property is shared by both protein-coding DNA and functional RNA-coding DNA. Non-coding sequences present a highly clustered inhomogeneity. We propose the hypothesis, corroborated with appropriate computer simulations, that this is due to the action of various transposition events accumulated for long time periods.