Intermolecular-Type Conical Intersections in Benzene Dimer.

The equilibrium and conical intersection geometries of the benzene dimer were computed in the framework of the conventional, linear-response time-dependent and spin-flipped time-dependent density functional theories (known as DFT, TDDFT and SF-TDDFT) as well as using the multiconfigurational complete active space self-consistent field (CASSCF) method considering the minimally augmented def2-TZVPP and the 6-31G(d,p) basis sets. It was found that the stacking distance between the benzene monomers decreases by about 0.5 Å in the first electronic excited state, due to the stronger intermolecular interaction energy, bringing the two monomers closer together. Intermolecular-type conical intersection (CI) geometries can be formed between the two benzene molecules, when (i) both monomer rings show planar deformation and (ii) weaker (approximately 1.6-1.8 Å long) C-C bonds are formed between the two monomers, with parallel and antiparallel orientation with respect to the monomer. These intermolecular-type CIs look energetically more favorable than dimeric CIs containing only one deformed monomer. The validity of the dimer-type CI geometries obtained by SF-TDDFT was confirmed by the CASSCF method. The nudged elastic band method used for finding the optimal relaxation path has confirmed both the accessibility of these intermolecular-type CIs and the possibility of the radiationless deactivation of the electronic excited states through these CI geometries. Although not as energetically favorable as the previous two CI geometries, there are other CI geometries characterized by the relative rotation of monomers at different angles around a vertical C-C axis.

New insight into catechol photochemistry: the role of different monomer and dimer configurations in radiation-less decay of the S1 electronic excited state.

The equilibrium geometries of the ground and first electronic excited states as well as the radiation-less deactivation channels of catechol in its monomer and dimer configurations were investigated using the standard linear-response and the spin-flipped TDDFT, multireference CASSCF as well as the similarity transformed equation-of-motion coupled cluster built with the domain-based local pair natural orbitals (DLPNO-STEOM-CCSD) methods. For the monomer, it was found that there is a new conical intersection geometry that can explain why catechol exhibits different photochemical behavior. This deactivation pathway involves almost simultaneously, an excited state intramolecular proton transfer between the two O atoms and an O-H bond breaks at the proton that is not between the two O atoms. From an energy balance point of view, these geometries are not associated with high potential barriers, so radiation-less relaxation can be achieved through these geometries. For the cyclohexane solvent, the lowest CI geometry shows an energy gap of about 4 kcal mol-1 lower than that found for acetonitrile, making the relaxation even more easier. In the case of catechol dimer structures, several so-called dimer-type CI geometries were found where both monomers exhibit substantial geometric distortions together with the formation of a weaker C-C bond between the two catechol monomers. These CI geometries are energetically more favorable and, in the case of aggregation processes, more likely to decay the excited states of the catechol through these radiation-less deactivation channels than those found for the monomer.

Calculation of the hole mobilities of the three homopolynucleotides, poly(guanilic acid), poly(adenilic acid), and polythymidine in the presence of water and Na+ ions.

Recent high resolution x-ray diffraction experiments have determined the structure of nucleosomes. In it 147 base pair long DNA B superhelix is wrapped around the eight nucleohistone proteins. They have found that there are many hydrogen-bonds (H-bonds) between the negative sites phosphate (PO4-) groups DNA, and first of all there is the positively charged lysine and arginine side chains of the histones. This means that there is a non-negligible charge transfer from DNA to the proteins causing a hole current in DNA and an electronic one in the proteins. If the relative positions of the two macromolecules change due to some external disturbances, the DNA moves away from the protein and can be read. If this happens simultaneously at several nucleosomes and at many places in chromatin (built up from the nucleosomes), undesired genetic information becomes readable. This final end can cause the occurrence of oncoproteins at an undesired time point which most probably disturbs the self-regulation of a differentiated cell. The connection of these chain of events with the initiation of cancer is obvious. To look into the details of these events we have used the detailed band structures of the four homopolynucleotides in the presence of water and natrium (Na+) ions calculated previously with the help of the ab initio Hartree-Fock crystal orbital method. We have found that in the case of three homopolynucleotides the width of their valence band is broad enough (approximately 10 times broader than the thermal energy at 300K) for the application of the simple deformation potential approximation for transport calculations. With the help of this we have determined the hole mobilities at 300K and 180K of poly(guanilic acid), poly(adenilic acid), and polythimidine (polycytidine has a too narrow valence band for the application of the deformation potential method). The obtained mobilities are large enough to allow Bloch-type conduction in these systems. At the end of the paper we discuss briefly the possible mechanism of charge transport in aperiodic DNA as a combination of Bloch-type conduction, hopping, and tunneling.