Dear Colleagues,

Today, many members of the scientific community are interested in charge transfer and transport in organic and biological systems such as carbon nanotubes, carbynes, porphyrins, proteins, enzymes, π-conjugated systems, nucleic acids (DNA, RNA), chromophores, to name just a few. Their electronic structure and their charge transfer and transport properties are being studied with the aim to understand their biological functions and their potential applications in nanotechnology. Transport implies the use of electrodes between which electric voltage is applied. Transfer means that the electron or hole, created, e.g., by reduction or oxidation at a specific site, moves to more favorable sites. Usually, a donor and an acceptor are connected at the ends of a system, which acts as a bridge. For example, DNA can be used as a molecular wire for charge transfer and transport. Favoring geometries and base-pair sequences, the use of non-natural bases, isomers and tautomers of the bases, among others, are being investigated. Structural fluctuation is another important factor which influences carrier movement through these systems. Charge transfer is, for example, relevant in DNA damage and repair and in discrimination between pathogenic and nonpathogenic mutations at an early stage. Charge transport can be used to probe DNA of different origin or organisms, mutations, and diseases. Charge transport in damaged DNA and under structural fluctuations has also been investigated.

• charge transfer
• charge transport
• polymers
• biopolymers
• carbon nanotubes
• carbynes
• porphyrins
• proteins
• enzymes
• π-conjugated systems
• nucleic acids
• DNA
• RNA
• chromophores

LCAO electronic structure of nucleic acid bases and other heterocycles and charge transfer parameters in B-DNA: effects of structural variability

Marilena Mantela^{^1} Constantinos Simserides^{^1} and Rosa Di Felice^{^2}

1 National and Kapodistrian University of Athens, Department of Physics, Panepistimiopolis, Zografos, GR-15784, Athens, Greece
2 University of Southern California, Department of Physics and Astronomy, Department of Quantitative and Computational Biology, 920 Bloom Walk, Los Angeles, CA 90089, USA

Abstract To describe the molecular electronic structure of nucleic acid bases and other heterocycles, we employ the linear
combination of atomic orbitals (LCAO) method, considering the molecular wavefunction as a linear combination of all valence
orbitals, i.e., 2s, 2px, 2py, 2pz orbitals for C, N and O atoms and 1s orbital for H atoms. Regarding the diagonal matrix
elements (aka on-site energies), we introduce a novel parametrization. For the non-diagonal matrix elements referring
to neighboring atoms, we employ  the Slater-Koster two-center interaction transfer integrals. We use Harrison-type expressions
with factors slightly modified relative to the original. We compare our LCAO predictions for the ionization and excitation
energies of heterocycles with those obtained from IP-EOMCCSD/aug-cc-pVDZ and CR-EOMCCSD(T)/aug-cc-pVDZ level of
theory as well as with available experimental values. Similarly, we calculate the transfer integrals between subsequent base
pairs. Taking into account all valence orbitals, we are in the position to treat deflection from the planar geometry, e.g., DNA
structural variability, a task impossible for the plane Hueckel LCAO (i.e., using only 2pz orbitals). We show a structural deformation example utilizing a 20mer evolved by own Molecular
Dynamics.