Thymine dimer splitting in the T<>T-G trinucleotide model system: a semiclassical dynamics and TD-DFT study

Surface functionalization of chitosan with 5-nitroisatin

Several possible configurations (CS/NI1-10) for the surface adsorption of 5-nitroisatin (NI) on the chitosan polymer (CS) were investigated using quantum mechanical methods in the gas and solution phases. The values of the binding energies indicate the energetic stability of these configurations. The solvation energies demonstrate that the solubility of NI and CS increases in the presence of each other. The role of hydrogen bonds in noncovalent surface functionalization was determined by AIM analysis. The mechanism of covalent surface functionalization and the explicit solvent effects (methanol) in this mechanism were investigated and it was determined that the covalent functionalization through Schiff base formation is possible. These findings, in addition to the biological applications of the chitosan Schiff bases and their complexes, led us to synthesize a new Schiff base from condensation reaction of CS and NI (CSB) together with its Ni(II) and Cu(II) complexes. The synthesized compounds were characterized by the elemental analysis, infrared spectroscopy (IR), thermogravimetry analysis (TGA) and differential scanning calorimetry (DSC). Also, optimized geometries, assignment of the IR vibrational bands as well as exploring of the frontier orbitals of the synthesized compounds have been calculated using density functional levels of theory.

Computational reference data for the photochemistry of cyclobutane pyrimidine dimers

The cis-syn cyclobutane pyrimidine dimer is one of the major classes of carcinogenic UV-induced DNA photoproducts. In this work, diverse high-level quantum-chemical methods were used to determine the spectroscopic properties of neutral (singlet and triplet) and charged (cation and anion) species of thymine dimers. Maps of potential energy, charge distribution, electron affinity, and ionization potential of the thymidine dimers were computed along the two dimerization coordinates for neutral and charged species, as well as for the singlet excited state. This set of data aims at providing consistent results computed with the same methods as for photodamage and repair. Based on these results, several different photo-, heat-, and charge-induced mechanisms of dimerization and repair are characterized and discussed. Additionally, a new stable dimer with methylmethylidene-hexahydropyrimidine structure was found in the S0 state.

Photoinduced processes in nucleic acids

Photoinduced processes in nucleic acids are phenomena of fundamental interest in diverse fields, from prebiotic studies, through medical research on carcinogenesis, to the development of bioorganic photodevices. In this contribution we survey many aspects of the research across the boundaries. Starting from a historical background, where the main milestones are identified, we review the main findings of the physical-chemical research of photoinduced processes on several types of nucleic-acid fragments, from monomers to duplexes. We also discuss a number of different issues which are still under debate.