Positive hole transfer between organic molecules of different classes in freon matrices

The processes of positive charge (hole) transfer between organic molecules of different classes occurring upon irradiation of their frozen freonic solutions at 77 K were studied by ESR spectroscopy. The efficiency of positive hole transfer was characterized by the “redistribution coefficient”, which was determined as ratio of concentrations of the radical cations of different compounds at equal concentrations of the parent neutral molecules. A very effective positive hole transfer to toluene was shown to occur for alkane-toluene pairs (K > 10). Meanwhile, much lower K values (～ 2 to 3) were observed for alkane-alkene pairs, in spite of a rather high difference in the ionization potentials (ca. 1 eV). This effect was explained by the conformation dispersion and distribution of environment configurations of ionized molecules for the alkane-alkene pairs. An effective positive hole transfer (K ～ 6) was observed for the pair dimethyl ether-acetone, where the conformation dispersion was absent, although the difference in ionization potentials for this pair was only 0.3 eV.     

Energy transfer in collisions between two vibrating molecules

We study vibrational energy transfer in inelastic collinear collisions between two diatomic molecules. The system is represented by two linearly driven parametric oscillators with a bilinear, time-dependent residual coupling between them. We account for the time evolution of the linearly driven parametric oscillators with an operator algebra, and use perturbation theory and basis expansions to include the residual coupling. Results are presented for H₂FH and N₂CO. Direct two-quantum transitions are found to be important even for low relative collision energies.     

Tunneling in the proton transfer between two water molecules

SCF CNDO calculations were performed for the species H₅O⁺₂ at several positions of the intervening proton and at interoxygen distances of 2.65, 2.70 and 2.75 Å. The energy profile was fitted to a potential energy function containing a quadratic term plus a gaussian. The eigenvalues and eigenvectors were obtained by using the variational method with the eigenfunctions of the parabolic potential as basis set. The results indicate that at 2.65 Å the top of the barrier is below the first energy level and that at 2.75 Å the first two energy levels are below the top of the barrier with the splitting of the symmetric-antisymmetric pair of 0.00132 au indicating that tunneling occurs at a frequency of 10¹⁴ reciprocal seconds.     

Orientation control of fluorescence resonance energy transfer using DNA as a helical scaffold

The efficiency of fluorescence resonance energy transfer (FRET) between two chromophores positioned at opposite ends of DNA base pair domains has been investigated. The base pair domain serves as a helical scaffold which defines both the distance between chromophores and the dihedral angle between their electronic transition dipole moments, each incremental base pair increasing the distance and stepping the dihedral angle. Fluorescence quantum yields and lifetimes have been determined for both the donor and acceptor chromophores. The experimental data are found to be in excellent accord with an oriented dipole model, rather than with the averaged dipole model conventionally assumed for FRET.     

Charge transfer in organic molecules for solar cells: theoretical perspective

This tutorial review primarily illustrates rate theories for charge transfer and separation in organic molecules for solar cells. Starting from the Fermi's golden rule for weak electronic coupling, we display the microcanonical and canonical rates, as well as the relationship with the Marcus formula. The fluctuation effect of bridges on the rate is further emphasized. Then, several rate approaches beyond the perturbation limit are revealed. Finally, we discuss the electronic structure theory for calculations of the electronic coupling and reorganization energy that are two key parameters in charge transfer, and show several applications.     

密度泛函理论研究2种新型染料分子的分子内电荷转移现象

采用量子化学方法研究了2种新型有机染料分子P1和P4,几何优化和基态性质计算采用B3LYP密度泛函,基组为6-311G(d).由于P1和P4分子中分别存在2个对称的吸电子基团,所以2个染料分子的电子结构存在明显的特点:2个紧邻简并最低空轨道(LowestUnoccupied Molecular Orbital,LUMO)轨道.P1和P4最高占据轨道(Highest Occupied Mo-lecular Orbital,HOMO)到LUMO轨道的跃迁能级差分别为2.79和3.26eV.同时,采用含时密度泛函方法(Time-Dependent Density Functional Theory,TDDFT)研究了2个染料分子的激发态性质.通过电荷差异密度理论方法(Charge Different Density,CDD)直观的展示了分子内电荷转移的现象.对于P1,电荷转移的方向是从苯甲酸基团到2个二氰乙烯基噻吩苯基团;对于P4,电荷是由2个二氰乙烯基联苯基团基团向苯甲酸基转移.     

Absolute rates of hole transfer in DNA

Absolute rates of hole transfer between guanine nucleobases separated by one or two A:T base pairs in stilbenedicarboxamide-linked DNA hairpins were obtained by improved kinetic analysis of experimental data. The charge-transfer rates in four different DNA sequences were calculated using a density-functional-based tight-binding model and a semiclassical superexchange model. Site energies and charge-transfer integrals were calculated directly as the diagonal and off-diagonal matrix elements of the Kohn-Sham Hamiltonian, respectively, for all possible combinations of nucleobases. Taking into account the Coulomb interaction between the negative charge on the stilbenedicarboxamide linker and the hole on the DNA strand as well as effects of base pair twisting, the relative order of the experimental rates for hole transfer in different hairpins could be reproduced by tight-binding calculations. To reproduce quantitatively the absolute values of the measured rate constants, the effect of the reorganization energy was taken into account within the semiclassical superexchange model for charge transfer. The experimental rates could be reproduced with reorganization energies near 1 eV. The quantum chemical data obtained were used to discuss charge carrier mobility and hole-transport equilibria in DNA.     

Resonant transfer of excitation between two molecules using Maxwell fields

The matrix element for the resonant transfer of excitation between two molecules possessing electric and magnetic multipole moments of arbitrary order is calculated using quantum electrodynamical response theory. A prerequisite of the method is the functional form for the lth order linear electric and magnetic multipole dependent electric displacement and magnetic field operators in the neighborhood of a molecule, whose derivation is also given. The initially unexcited species is viewed as a test body accepting energy resonantly via coupling to the Maxwell fields of the excited multipole source molecule. The generalized electric-electric multipole contribution to the matrix element is shown to agree with an earlier calculation using time-dependent perturbation theory. As an application involving both electric and magnetic terms, the rate of excitation transfer between two chiral molecules is computed and found to depend on the handedness of each species.     

Temperature dependence for the rate of hole transfer in DNA: Nonadiabatic regime

The positive charge transfer in DNA is investigated, using the first principle treatment of the electron-vibrational interaction. We show that rearrangements of atoms belonging to base pairs induced by charge transfer are essentially quantum mechanical in nature. Particularly at room temperature, around half of the rearrangements occur via quantum tunneling, while the other half takes place via thermally activated transitions. This effect reduces activation energies for charge transfer between both AT and GC pairs by a factor of two compared to their classical values. These behaviors are described within small polaron theory for the non-adiabatic charge transfer and compared to the experimental data and previous theoretical studies.     

Hole transfer in DNA and photosensitized DNA damage: importance of adenine oxidation

Photosensitized DNA damage reactions were investigated for two well-known DNA-damaging photosensitizers (Sens), naphthalimide (NI) and napthaldiimide (NDI), which have similar photophysical properties but differ in their redox properties. NI and NDI derivatives (NIN, NDIN), which have cationic side chains and electrostatically binding to DNA due to favorable electrostatic interactions between the negatively charged phosphate groups of DNA and cationic groups, and NIP and NDIP, which possess phosphate groups and do not bind to DNA, were synthesized. NIN and NDIN can oxidize A and G via their singlet excited state, and NDIP oxidizes A and G via its triplet excited state, whereas NIP oxidizes only G. A combination of laser flash photolysis kinetic studies and quantitative HPLC analyses of photosensitized DNA damage was performed for several DNA sequences in the presence of Sens. NIN, NDIN, and NDIP, which oxidizes A, caused significant DNA damage upon photoirradiation, and DNA damage yield increased with the length of the consecutive A stretch. In contrast, NIP, which oxidizes only G, caused only moderate damage to DNA and showed no preference for the consecutive A sequences. These results clearly demonstrate the importance of A-oxidation, especially in consecutive A sequences, which triggers the rapid hole transfer between A's.     

Hole and excess electron transfer dynamics in DNA

Charge transfer in DNA attracts substantial attention from researchers in a wide group of fields such as bioscience, nanotechnology and physical chemistry. It is well known that both positive and negative charges, which are holes and excess electrons, respectively, contribute to the charge transfer in DNA. In the case of hole transfer in DNA, detailed mechanisms and dynamical parameters have been estimated by means of time-resolved spectroscopic methods and product analysis. On the other hand, detailed dynamics of excess electron transfer have not been established yet, although several aspects have been revealed by the continuous efforts of various research groups. In the present Perspective, studies on the charge transfer dynamics in DNA are summarized.     

Master equation approach to vibrational energy transfer between two diatomic molecules

In this paper a semiclassical non-markovian master equation is derived. We begin by using the well-known tetradic form of the Liouville equation for a reduced density operator. By projecting the diagonal matrix elements of the operator, we obtain an infinite-order master equation. This equation is then applied in the lowest-order approximation to collinear collisions between the diatomic molecules: H₂H₂, N₂N₂ and Cl₂Cl₂. With an assumed form of the interaction potential for such a problem we have also derived an analytical expression for the V—V transition probabilities. They are then calculated over a wide range of velocities of the colliding molecules and compared with exact semiclassical ones. An excellent agreement of the results is found for small velocities (i.e. υ ≈ 10⁴ cm/s). For larger values of υ (≈ 10⁵ cm/s) the results obtained from the master equation approach agree with the exact ones only in the low-velocity range for light molecules and low oscillatory states.     

High order corrections to vibrational energy transfer in collisions between two diatomic molecules

This paper analyses the validity of the first Born approximation for the study of the vibrational transitions brought about during a collision between two diatomic molecules. The work shows the importance of the alteration of the molecular parameters during the collision and the anharmonicity of the potential of the two molecules on the transfers VT with one quantum and VV with two quanta.     

Supramolecular helical porphyrin arrays using DNA as a scaffold

A diphenyl porphyrin substituted nucleotide was incorporated site specifically into DNA, leading to helical stacked porphyrin arrays in the major groove of the duplexes. The porphyrins show an electronic interaction which is significantly enhanced compared to the analogous tetraphenyl porphyrin (TPP) as shown in the large exciton coupling of the porphyrin B-band absorbance. Analogous to the TPP-DNA, an induced helical secondary structure is observed in the single strand porphyrin-DNA. The modified DNA can be hybridised to an immobilised complementary strand leading to fluorescent beads.     

Electronic excitation energy transfer between molecules of carbocyanine dyes in complexes with DNA

Electronic excitation energy transfer has been carried out between molecules of carbocyanine dyes bound noncovalently to DNA. 3,3′,9-Triethyl-5,5′-dimethyloxacarbocyanine iodide was used as an energy donor and 3,3′-diethylthiacarbocyanine iodide as an acceptor dye. In this process, the band belonging to the donor is observed in the fluorescence excitation spectrum of the acceptor. Donor fluorescence quenching by the acceptor in the presence of DNA was studied. The results of the experiments are discussed in terms of the Dye-DNA stoichiometric complex formation and with respect to concentrating the dyes in the microphase (pseudophase) of the biopolymer.     

Chiral coordination polymer as a luminescence sensor for small organic molecules

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Intercalation of organic dye molecules into double-stranded DNA. Part 2: the annelated quinolizinium ion as a structural motif in DNA intercalators

DNA intercalators represent an important class of compounds with a high potential as DNA-targeting drugs. In this review it is demonstrated that annelated quinolizinium derivatives such as coralyne and derivatives thereof intercalate into DNA and that this structural motif allows several variations of the substitution pattern without loss of intercalating properties. The commonly applied methods for the evaluation of the DNA association, mainly spectroscopic studies, are pointed out. In addition, studies on the biological activities of annelated quinolizinium derivatives, such as topoisomerase poisoning or cell toxicity, are highlighted.     

Hole transfer energetics in structurally distorted DNA: the nucleosome core particle

The dynamics of long-range hole transport (HT) through DNA are critically dependent on the relative energies of guanine radical cation states. Electrostatic contacts with protein fragments and changes in the secondary structure of the DNA helix are expected to directly influence the stability of a guanine radical cation. This expectation is especially relevant when considering DNA HT in the eukaryotic nucleus, where DNA is condensed into nucleosome core particles (NCPs), the fundamental building blocks of chromatin. Using quantum-chemical calculations, we consider how the electrostatic interactions between the DNA nucleobases and the surrounding protein and water atoms and the structural changes in DNA arising from compaction into a NCP affect the energetics of hole transfer between guanine sites. We find that structural distortions of DNA can have dramatic consequences for the stability of a guanine radical cation, and therefore, these effects must be taken into account during the modeling of in vivo DNA HT and in the interpretation of experimental findings. When the electrostatic potential arising from the water and basic histone proteins is included we find that DNA-histone contacts, particularly between arginine residues and the DNA minor groove, destabilize the hole state on specific guanine residues. Therefore, contacts between the DNA nucleobases and basic amino acids have the potential to perturb the sites of preferred hole stability in DNA.