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 wave function as a linear combination of all valence orbitals, i.e., 2s, 2p, 2p, 2p orbitals for C, N, and O atoms and 1s orbital for H atoms. Regarding the diagonal matrix elements (also known as on-site energies), we introduce a novel parameterization. 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 Ionization Potential Equation of Motion Coupled Cluster with Singles and Doubles (IP-EOMCCSD)/aug-cc-pVDZ level of theory and Completely Normalized Equation of Motion Coupled Cluster with Singles, Doubles, and non-iterative Triples (CR-EOMCCSD(T))/aug-cc-pVDZ level of theory, respectively, (vertical values), as well as with available experimental data. Similarly, we calculate the transfer integrals between subsequent base pairs, to be used for a Tight-Binding (TB) wire model description of charge transfer and transport along ideal or deformed B-DNA. 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 Hückel approach (i.e., using only 2p orbitals). We show the effects of structural deformations utilizing a 20mer evolved by Molecular Dynamics.
Highlights
The study of the electronic structure of organic heterocyclic molecules has been of interest for the scientific community for decades, especially since the establishment of investigation methods based on quantum mechanics
Among other theoretical and experimental attempts, the electronic structure of single DNA molecules has been resolved by transverse scanning tunneling spectroscopy and assigned to groups of orbitals originating from the molecular entities, i.e., nucleobases, backbone, counterions [12]
The rest of this article is organized in the following way: In Section 2, we develop the novel Linear Combination of Atomic Orbitals (LCAO) parameterization that includes all valence orbitals for nucleic acid bases (Section 2.1) and base pairs (Section 2.2)
Summary
The study of the electronic structure of organic heterocyclic molecules has been of interest for the scientific community for decades, especially since the establishment of investigation methods based on quantum mechanics. We calculate the ionization and excitation energies of nucleic acid bases and similar molecules as well as assemblies of DNA bases using a semi-empirical Linear Combination of Atomic Orbitals (LCAO) method that includes all valence orbitals with a novel parameterization developed by us. Using this approach, we obtain electronic parameters for charge (electron or hole) transfer along DNA, which can be employed to model electron and hole conductivity. The same treatment developed for DNA bases is applicable to other purines, pyrimidines, and similar molecules
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