Photophysical Properties of [Ru(phen)2(dppz)]2+ Intercalated into DNA: An Integrated Car−Parrinello and TDDFT Study

Electronic structures and spectroscopic properties of rhenium (I) tricarbonyl photosensitizer: [Re(4,4'-(COOEt)2-2,2'-bpy)(CO)3py]PF6

The ground state and lowest triplet-state structures of [Re(4,4'-(COOEt)(2)-2,2'-bpy)(CO)(3)py]PF(6) photosensitizer (bpy=bipyridine, py=pyridine) have been studied with density functional theory (DFT). Time-dependent density functional theory (TD-DFT) was carried out to predict the photophysical properties of the photosensitizer. The effects of the solvents were evaluated using the conductor-like polarizable continuum (CPCM) method in dichloromethane, chloroform, acetonitrile, acetone, ethanol and dimethylsulfoxide. The electronic transition energies computed with BLYP, MPWPW91, B3LYP and MPW1PW91 functionals are compared with the experimental spectra. Based on the calculated excited energies, the experimental absorption maximum is assigned as metal-to-ligand charge transfer (MLCT) and ligand-to-ligand charge transfer (LLCT) mixed transition, and the luminescence originates from the lowest triplet state that is ascribed as the mixed transition of MLCT/LLCT.

Alignment of the dye's molecular levels with the TiO(2) band edges in dye-sensitized solar cells: a DFT-TDDFT study

We present a theoretical study of the lineup of the LUMO of Ru(II)-polypyridyl (N3 and N719) molecular dyes with the conduction band edge of a TiO(2) anatase nanoparticle. We use density functional theory (DFT) and the Car-Parrinello scheme for efficient optimization of the dye-nanoparticle systems, followed by hybrid B3LYP functional calculations of the electronic structure and time-dependent DFT (TDDFT) determination of the lowest vertical excitation energies. The electronic structure and TDDFT calculations are performed in water solution, using a continuum model. Various approximate procedures to compute the excited state oxidation potential of dye sensitizers are discussed. Our calculations show that the level alignment for the interacting nanoparticle-sensitizer system is very similar, within about 0.1 eV, to that for the separated TiO(2) and dye. The excellent agreement of our results with available experimental data indicates that the approach of this work could be used as an efficient predictive tool to help the optimization of dye-sensitized solar cells.

Physical nature of ethidium and proflavine interactions with nucleic acid bases in the intercalation plane

On the basis of the crystallographic structures of three nucleic acid intercalation complexes involving ethidium and proflavine, we have analyzed the interaction energies between intercalator chromophores and their four nearest bases, using a hybrid variation-perturbation method at the second-order Møller-Plesset theory level (MP2) with a 6-31G(d,p) basis set. A total MP2 interaction energy minimum precisely reproduces the crystallographic position of the ethidium chromophore in the intercalation plane between UA/AU bases. The electrostatic component constitutes the same fraction of the total energy for all three studied structures. The multipole electrostatic interaction energy, calculated from cumulative atomic multipole moments (CAMMs), was found to converge only after including components above the fifth order. CAMM interaction surfaces, calculated on grids in the intercalation planes of these structures, reasonably reproduce the alignment of intercalators in crystal structures; they exhibit additional minima in the direction of the DNA grooves, however, which also need to be examined at higher theory levels if no crystallographic data are given.

Controlling Phosphorescence Color and Quantum Yields in Cationic Iridium Complexes: A Combined Experimental and Theoretical Study

We report a combined experimental and theoretical study on cationic Ir(III) complexes for OLED applications and describe a strategy to tune the phosphorescence wavelength and to enhance the emission quantum yields for this class of compounds. This is achieved by modulating the electronic structure and the excited states of the complexes by selective ligand functionalization. In particular, we report the synthesis, electrochemical characterization, and photophysical properties of a new cationic Ir(III) complex, [Ir(2,4-difluorophenylpyridine)2(4,4'-dimethylamino-2,2'-bipyridine)](PF(6)) (N969), and compare the results with those reported for the analogous [Ir(2-phenylpyridine)2(4,4'-dimethylamino-2,2'-bipyridine)](PF(6)) (N926) and for the prototype [Ir(2-phenylpyridine)2(4,4'-tert-butyl-2,2'-bipyridine)](PF(6)) complex, hereafter labeled N925. The three complexes allow us to explore the (C/\N) and (N/\N) ligand functionalization: considering N925 as a reference, we investigate in N926 the effect of electron-releasing substituents on the bipyridine ligand, while in N969, we investigate the combined effect of electron-releasing substituents on the bipyridine ligand and the effect of electron-withdrawing substituents on the phenylpyridine ligands. For N969 we obtain blue-green emission at 463 nm with unprecedented high quantum yield of 85% in acetonitrile solution at room temperature. To gain insight into the factors responsible for the emission color change and the different quantum yields, we perform DFT and TDDFT calculations on the ground and excited states of the three complexes, characterizing the excited-state geometries and including solvation effects on the calculation of the excited states. This computational procedure allows us to provide a detailed assignment of the excited states involved in the absorption and emission processes and to rationalize the factors determining the efficiency of radiative and nonradiative deactivation pathways in the investigated complexes. This work represents an example of electronic structure-driven tuning of the excited-state properties, thus opening the way to a combined theoretical and experimental strategy for the design of new iridium(III) phosphors with specific target characteristics.

Chirality as a tool in nucleic acid recognition: principles and relevance in biotechnology and in medicinal chemistry

The understanding of the interaction of chiral species with DNA or RNA is very important for the development of new tools in biology and of new drugs. Several cases in which chirality is a crucial point in determining the DNA binding mode are reviewed and discussed, with the aim of illustrating how chirality can be considered as a tool for improving the understanding of mechanisms and the effectiveness of nucleic acid recognition. The review is divided into two parts: the former describes examples of chiral species interacting with DNA: intercalators, metal complexes, and groove binders; the latter part is dedicated to chirality in DNA analogs, with discussion of phosphate stereochemistry and chirality of ribose substitutes, in particular of peptide nucleic acids (PNAs) for which a number of works have been published recently dealing with the effect of chirality in DNA recognition. The discussion is intended to show how enantiomeric recognition originates at the molecular level, by exploiting the enormous progresses recently achieved in the field of structural characterization of complexes formed by nucleic acid with their ligands by crystallographic and spectroscopic methods. Examples of application of the DNA binding molecules described and the role of chirality in DNA recognition relevant for biotechnology or medicinal chemistry are reported.

Ab initio molecular dynamics of heme in cytochrome c

Ab initio molecular dynamics (AIMD) calculations, based on the Car-Parrinello method, have been carried out for three models of heme c that is present in cytochrome c. Both the reduced (Fe(II)) and oxidized (Fe(III)) forms have been analyzed. The simplest models (1R and 1O, respectively) consist of a unsubstituted porphyrin (with no side chains) and two axially coordinated imidazole and ethylmethylthioether ligands. Density functional theory optimizations of these models confirm the basic electronic features and are the starting point for building more complex derivatives. AIMD simulations were performed after reaching the thermal stability at T = 300 K. The evolution of the Fe-L(ax) bond strengths is examined together with the relative rotations of the imidazole and methionine about the axial vector, which appear rather independent from each other. The next models (2R and 2O) contain side chains at the heme to better simulate the actual active site. It is observed that two adjacent propionate groups induce some important effects. The axial Fe-Sdelta bond is only weakened in 2R but is definitely cleaved in the oxidized species 2O. Also the mobility of the Im ligand seems to be reduced by the formation of a strong hydrogen bond that involves the Im Ndelta1-Hdelta1 bond and one carboxylate group. In 2O the interaction becomes so strong that a proton transfer occurs and the propionic acid is formed. Finally, the models 3 include a free N-methyl-acetamide molecule to mimic a portion of the protein backbone. This influences the orientation of carboxylate groups and limits the amount of their hydrogen bonding with the Im ligand. Residual electrostatic interactions are maintained, which are still able to modulate the dissociation of the methionine from the heme.

Theoretical Studies on the Excited States, DNA Photocleavage, and Spectral Properties of Complex [Ru(phen)2(6-OH-dppz)]2+

The structures and related properties of the complex [Ru(phen)2(6-OH-dppz)]2+ (phen = 1,10-phenanthroline; dppz = dipyrido [3,2-a:2',3'-c]phenazine) in the ground state (S0), the first singlet excited state (S1), and the first triplet excited state (T1) have been studied using density functional theory (DFT), time-dependent (TD) DFT, Hartree-Fock (HF), and configuration interaction singles (CIS) methods. Three electronic absorption-spectral bands (1MLCT, 1LL, and 1LL) lying in the range of 250-550 nm in vacuo and in aqueous solution were theoretically calculated, simulated, and assigned with TDDFT method. In particular, the theoretical results show the following: (1) The positive charges of central Ru atom in the excited states (S1 and T1) are greatly increased relative to those in the ground state (S0), and thus the Ru atom in the excited states can be regarded as Ru(III). (2) The positive charges on the main ligand (6-OH-dppz) in the excited states are considerably reduced, and thus the interaction between the main ligand (intercalative ligand) and DNA base pairs is considerably weakened. (3) The geometric structures in excited states are also distorted, resulting in obvious increase in the coordination bond length. It is advantageous to the complex forming a high oxidizing center (i.e., Ru(III) ion). On the basis of these results, a theoretical explanation on photoinduced oxidation reduction mechanism of DNA photocleavage by [Ru(phen)2(6-OH-dppz)](2+) has been presented.

Interaction of Lambda- and Delta-[Ru(bpy)2(pbmz)](PF6)2 with the oligonucleotide duplex d(CGCGAATTCGCG)2

The interaction of the enantiomeric complexes Lambda- and Delta-[Ru(bpy)(2)(pbmz)](PF(6))(2) (bpy=2,2'-bipyridine, pbmz=2-(2'-pyridyl)benzimidazole) with the DNA duplex d(CGCGAATTCGCG)(2) was investigated by means of 2D NMR techniques. The synthesis of the enantiomers was based on the optically pure complexes Lambda- and Delta-[Ru(bpy)(2)(py)(2)](2+) and were characterized by CD and NMR spectroscopy. NMR data indicate that both enantiomers bind weakly to the oligonucleotide, approaching from the minor groove at the centre of the helix. The perturbation of the B-DNA conformation is minor with an apparent absence of enantioselectivity. Molecular modelling calculations in conjunction with the NOE data support the suggestion that more than one binding modes are present. The imidazole amine group of the pbmz ligand is probably hydrogen bonded to the DNA phosphodiesteric backbone at the AATT step, and this may provide an explanation for the diminished enantioselectivity observed.

Density Functional Theory/Time-dependent DFT Studies on the Structures, Trend in DNA-binding Affinities, and Spectral Properties of Complexes [Ru(bpy)2(p-R-pip)]2+ (R = −OH, −CH3, −H, −NO2)

Studies on the electronic structures and trend in DNA-binding affinities of a series of Ru(II) complexes [Ru(bpy)2(p-R-pip)]2+ (bpy = 2,2-bipyridine; pip = 2-phenylimidazo[4,5-f] [1,10]-phenanthroline; R = -OH, -CH3, -H, -NO2) 1-4 have been carried out, using the density functional theory (DFT) at the B3LYP/LanL2DZ level. The electronic absorption spectra of these complexes were also investigated using time-dependent DFT (TDDFT) at the B3LYP//LanL2DZ/6-31G level. The computational results show that the substituents on the parent ligand (pip) have a significant effect on the electronic structures of the complexes, in particular, on the energies of the lowest unoccupied molecular orbital (LUMO) and near some unoccupied molecular orbitals (LUMO+x, x = 1-4). With the increase in electron-withdrawing ability of the substituent in this series, the LUMO+x (x = 0-4) energies of the complexes are substantially reduced in order, for example, epsilon(LUMO)(1) approximately epsilon(LUMO)(2) > epsilon(LUMO)(3) > epsilon(LUMO)(4), whereas the pi-component populations of the LUMO+x (x = 0-4) are not substantially different. Combining the consideration of the bigger steric hindrance of complex 2, the trend in DNA-binding affinities (K(b)) of the complexes, that is, K(b)(2) < K(b)(1) < K(b)(3) < K(b)(4) can be reasonably explained. In addition, the experimental singlet metal-to-ligand charge transfer ((1)MLCT) spectra of these complexes can be well simulated and discussed by the TDDFT calculations.

Combined Experimental and DFT-TDDFT Computational Study of Photoelectrochemical Cell Ruthenium Sensitizers

We report a combined experimental and computational study of several ruthenium(II) sensitizers originated from the [Ru(dcbpyH(2))(2)(NCS)(2)], N3, and [Ru(dcbpyH(2))(tdbpy)(NCS)(2)], N621, (dcbpyH(2) = 4,4'-dicarboxy-2,2'-bipyridine, tdbpy = 4,4'-tridecyl-2,2'-bipyridine) complexes. A purification procedure was developed to obtain pure N-bonded isomers of both types of sensitizers. The photovoltaic data of the purified N3 and N621 sensitizers adsorbed on TiO(2) films in their monoprotonated and diprotonated state, exhibited remarkable power conversion efficiency at 1 sun, 11.18 and 9.57%, respectively. An extensive Density Functional Theory (DFT)-Time Dependent DFT study of these sensitizers in solution was performed, investigating the effect of protonation of the terminal carboxylic groups and of the counterions on the electronic structure and optical properties of the dyes. The calculated absorption spectra are in good agreement with the experiment, thus allowing a detailed assignment of the UV-vis spectral features of the two types of dyes. The computed alignments of the molecular orbitals of the different complexes with the band edges of a model TiO(2) nanoparticle provide additional insights into the electronic factors governing the efficiency of dye-sensitized solar cell devices.