LCAO Electronic Structure of Nucleic Acid Bases and Other Heterocycles and Transfer Integrals in B-DNA, Including Structural Variability

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, 2px, 2py, 2pz 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 2pz orbitals). We show the effects of structural deformations utilizing a 20mer evolved by Molecular Dynamics.

Interactions of Thymine and Uracil with Copper, Cobalt and Silver Ferrocyanides and the Implications in Chemical Evolution

Effects on pH based adsorption of nucleic acid bases (thymine and uracil) at two different concentrations 1 x 10-4 M and 1 x 10-5 M on copper, cobalt and silver ferrocyanides were studied over a pH range (1.0 – 10.0) at temperature 30±1ºC. The progress of adsorption was followed spectrophotometrically by measuring the UV absorbance of the nucleic acid base solutions at their corresponding max. Maximum adsorptions were found at neutral pH for both thymine and uracil. Effects of concentrations on adsorption of thymine and uracil on copper, cobalt and silver ferrocyanides were studied in a concentration range 10-4 – 10-5 M at neutral pH 7.0 ± 0.1 and at temperature 30±1°C. The interaction followed the Langmuir type of adsorption in general in the concentration range of 10-4 to 10-5 M of thymine and uracil solution. The uptake of nucleic bases on metal ferrocyanides followed the order of CuFc > AgFc > CoFc for the adsorption of thymine and CuFc > CoFc > AgFc for the adsorption of uracil. Effects of the presence of salts on the adsorption of thymine and uracil on metal ferrocyanides also had been studied. The insoluble metal ferrocyanides’ interaction with biomolecules must have either formed metal complexes or could have enhanced the formation of biopolymers in fluctuating environment.

Interactions of selected organic molecules with a blue phosphorene monolayer: self-assembly, solvent effect, enhanced binding and fixation through coadsorbed gold clusters

In this paper, we investigate the interaction of aminoacids and nucleic acid bases with pristine/bare and gold cluster covered blue phospherene monolayers using ab initio density functional theory.