Theoretical insights into dopamine photochemistry adsorbed on graphene-type nanostructures.

The equilibrium geometry structures and light absorption properties of the dopamine (DA) and dopamine-o-quinone (DAQ) adsorbed on the graphene surface have been investigated using the ground state and linear-response time-dependent density functional theories. Two types of graphene systems were considered, a rectangular form of hexagonal lattice with optimized C-C bond length as the model system for graphene nanoparticles (GrNP) and a similar system but with fixed C-C bond length (1.42 Å) as the model system for graphene 2D sheet (GrS). The analysis of the vertical excitations showed that three types of electronic transitions are possible, namely, localized on graphene, localized on the DA or DAQ, and charge transfer (CT). In the case of the graphene-DA complex, the charge transfer excitations were characterized by the molecule-to-surface (MSCT) character, whereas the graphene-DAQ was characterized by the reverse, i.e. surface-to-molecule (SMCT). The difference between the two cases is given by the presence of an energetically low-lying unoccupied orbital (LUMO+1) that allows charge transfer from the surface to the molecule in the case of DAQ. However, it was also shown that the fingerprints of excited electronic states associated with the adsorbed molecules cannot be seen in the spectrum, as they are mostly suppressed by the characteristic spectral shape of graphene.

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.

Theoretical modeling of the singlet-triplet spin transition in different Ni(II)-diketo-pyrphyrin-based metal-ligand octahedral complexes.

The structural stability, charge transfer effects and strength of the spin-orbit couplings in different Ni(ii)-ligand complexes have been studied at the DFT (B3LYP and CAM-B3LYP) and coupled cluster (DLPNO-CCSD(T)) levels of theory. Accordingly, two different, porphyrin- and diketo-pyrphyrin-based four-coordination macrocycles as planar ligands as well as pyridine (or pyrrole) and mesylate anion molecular groups as vertical ligands were considered in order to build metal-organic complexes with octahedral coordination configurations. For each molecular system, the identification of equilibrium geometries and the intersystem crossing (the minimum energy crossing) points between the potential energy surfaces of the singlet and triplet spin states is followed by computing the spin-orbit couplings between the two spin states. Structures, based on the diketo-pyrphyrin macrocycle as the planar ligand, show stronger six-coordination metal-organic complexes due to the extra electrostatic interaction between the positively charged central metal cation and the negatively charged vertical ligands. The results also show that the magnitude of the spin-orbit coupling is influenced by the atomic positions of deprotonations of the ligands, and implicitly the direction of the charge transfer between the ligand and the central metal ion.

Theoretical Study of Light-Induced Crosslinking Reaction Between Pyrimidine DNA Bases and Aromatic Amino Acids.

Low-lying electronic excited states and their relaxation pathways as well as energetics of the crosslinking reaction between uracil as a model system for pyrimidine-type building blocks of DNA and RNA and benzene as a model system for aromatic groups of tyrosine (Tyr) and phenylalanine (Phe) amino acids have been studied in the framework of density functional theory. The equilibrium geometries of the ground and electronic excited states as well as the crossing points between the potential energy surfaces of the uracil-benzene complex were computed. Based on these results, different relaxation pathways of the electronic excited states that lead to either back to the initial geometry configuration or the dimerization between the six-membered rings of the uracil-benzene complex have been identified, and the energetic conditions for their occurrence are discussed. It can be concluded that the DNA-protein crosslinking reaction can be induced by the external electromagnetic field via the dimerization reaction between the six-membered rings of the uracil-benzene pair at the electronic excited-state level of the complex. In the case of the uracil-phenol complex, the configuration of the cyclic adduct (dimerized) conformation is less likely to be formed.