Development of donor-acceptor modified DNA hairpins for the investigation of charge hopping kinetics in DNA

Investigation of hole or excess electron hopping in DNA is mostly performed based on yield studies, in which an injector modified DNA duplex is irradiated to continuously inject either holes or electrons into the duplex. Observed is a chemical reaction of a "probe" molecule, which can be either one of the two purine bases or a different trap molecule positioned at various distances. The next step in the field will be the direct time resolution of the hole or electron transfer kinetics in DNA. Herein we describe the development of defined donor-DNA-acceptor systems, with properties that may allow time resolved electron and hole transfer studies in stably folded DNA structures.     

Dynamics and energetics of single-step hole transport in DNA hairpins

The dynamics of single-step hole transport processes have been investigated in a number of DNA conjugates possessing a stilbenedicarboxamide electron acceptor, a guanine primary donor, and several secondary donors. Rate constants for both forward and return hole transport between the primary and secondary donor are obtained from kinetic modeling of the nanosecond transient absorption decay profiles of the stilbene anion radical. The kinetic model requires that the hole be localized on either the primary or the secondary donor and not delocalized over both the primary and the secondary donor. Rate constants for hole transport are found to be dependent upon the identity of the secondary donor, the intervening bases, and the location of the secondary donor in the same strand as the primary donor or in the complementary strand. Rate constants for hole transport are much slower than those for the superexchange process used to inject the hole on the primary donor. This difference is attributed to the larger solvent reorganization energy for charge transport versus charge separation. The hole transport rate constants obtained in these experiments are consistent with experimental data for single-step hole transport from other transient absorption studies. Their relevance to long-distance hole migration over tens of base pairs remains to be determined. The forward and return hole transport rate constants provide equilibrium constants and free energies for hole transport equilibria. Secondary GG and GGG donors are found to form very shallow hole traps, whereas the nucleobase deazaguanine forms a relatively deep hole trap. This conclusion is in accord with selected strand cleavage data and thus appears to be representative of the behavior of holes in duplex DNA. Our results are discussed in the context of current theoretical models of hole transport in DNA.     

Temperature dependence of charge separation and recombination in porphyrin oligomer-fullerene donor-acceptor systems

Electron-transfer reactions are fundamental to many practical devices, but because of their complexity, it is often very difficult to interpret measurements done on the complete device. Therefore, studies of model systems are crucial. Here the rates of charge separation and recombination in donor-acceptor systems consisting of a series of butadiyne-linked porphyrin oligomers (n = 1-4, 6) appended to C(60) were investigated. At room temperature, excitation of the porphyrin oligomer led to fast (5-25 ps) electron transfer to C(60) followed by slower (200-650 ps) recombination. The temperature dependence of the charge-separation reaction revealed a complex process for the longer oligomers, in which a combination of (i) direct charge separation and (ii) migration of excitation energy along the oligomer followed by charge separation explained the observed fluorescence decay kinetics. The energy migration is controlled by the temperature-dependent conformational dynamics of the longer oligomers and thereby limits the quantum yield for charge separation. Charge recombination was also studied as a function of temperature through measurements of femtosecond transient absorption. The temperature dependence of the electron-transfer reactions could be successfully modeled using the Marcus equation through optimization of the electronic coupling (V) and the reorganization energy (λ). For the charge-separation rate, all of the donor-acceptor systems could be successfully described by a common electronic coupling, supporting a model in which energy migration is followed by charge separation. In this respect, the C(60)-appended porphyrin oligomers are suitable model systems for practical charge-separation devices such as bulk-heterojunction solar cells, where conformational disorder strongly influences the electron-transfer reactions and performance of the device.     

Impact of bridging units on the dynamics of photoinduced charge generation and charge recombination in donor-acceptor dyads.

We estimate, at a full quantum-chemical level, the various molecular parameters governing the rate of photoinduced charge generation and charge recombination in model organic structures containing a donor and an acceptor unit in view of the possible use of such systems in organic solar cells. The rate of through-space excitation dissociation, as predicted in the framework of the Marcus-Levich-Jortner theory, is found to be low in comparison to intramolecular decay processes when the donor and acceptor molecules are lying in a head-to-tail arrangement and high when the donor and acceptor molecules are superimposed in a cofacial arrangement. The charge separation rates for side-by-side donor-acceptor dyads are significantly increased by promoting through-bond interactions in covalently linked donor and acceptor units. This has motivated a detailed quantitative analysis of the influence of the nature, size, and conformation of the bridging moiety on the calculated transfer rates.     

Investigation of the pathways of excess electron transfer in DNA with flavin-donor and oxetane-acceptor modified DNA hairpins

Oxetane is a potential intermediate that is enzymatically formed during the repair of (6-4) DNA lesions by special repair enzymes (6-4 DNA photolyases). These enzymes use a reduced and deprotonated flavin to cleave the oxetane by single electron donation. Herein we report synthesis of DNA hairpin model compounds containing a flavin as the hairpin head and two different oxetanes in the stem structure of the hairpin. The data show that the electron moves through the duplex even over distances of 17 A. Attempts to trap the moving electron with N2O showed no reduction of the cleavage efficiency showing that the electron moves through the duplex and not through solution. The electron transfer is sequence dependent. The efficiency is reduced by a factor of 2 in GC rich DNA hairpins.     

Effect of the excitation wavelength on the ultrafast charge recombination dynamics of donor-acceptor complexes in polar solvents

The effect of the excitation wavelength on the charge recombination (CR) dynamics of several donor-acceptor complexes (DACs) composed of benzene derivatives as donors and of tetracyanoethylene or pyromellitic dianhydride as acceptors has been investigated in polar solvents using ultrafast time-resolved spectroscopy. Three different wavelength effects have been observed. (1) With complexes exhibiting two well-separated charge-transfer bands, the CR dynamics was found to be slower by a factor of about 1.5 upon excitation in the high-energy band. This effect was measured in both fast and slow relaxing solvents and was discussed in terms of different DAC geometries. (2) When the CR is faster than diffusive solvation, a slowing down of the CR with increasing excitation wavelength accompanied by an increase of the nonexponential character of the dynamics was measured. This effect appears only when exciting on the red edge of the charge-transfer absorption band. (3) When the driving force for CR is small, both nonequilibrium (hot) and thermally activated CR pathways can be operative. The results obtained with such a complex indicate that the relative contribution of these two paths depends on the excitation wavelength.     

Effects of alkyl substitution on the energetics of enolate anions and radicals.

The photoelectron spectra of the structural isomers of the three- and four-carbon enolate anions, n-C3H5O(-), i-C3H5O(-), n-C4H7O(-), s-C4H7O(-), and i-C4H7O(-) have been measured at 355 nm. Both the X(2A' ') ground and A(2A') first excited states of the corresponding radicals were accessed from the X(1A') ground state of the enolate anions. The separation energies of the ground and first excited states (T0) were determined: T0[(E)-n-C3H5O] = 1.19 +/- 0.02 eV, T0[(Z)-n-C3H5O] = 0.99 +/- 0.02 eV, T0[i-C3H5O] = 1.01 +/- 0.02 eV, T0[n-C4H7O] = 1.19 +/- 0.02 eV, T0[(2,3)-s-C4H7O] = 1.25 +/- 0.02 eV, T0[(1,2)-s-C4H7O] = 0.98 +/- 0.02 eV, and T0[i-C4H7O] = 1.36 +/- 0.02 eV. The effects of alkyl substitution on the vibronic structure and energetics previously observed in the vinoxy radical are discussed. The X(1A')-X(2A' ') relative stability is strongly influenced by substitution whereas the X(1A')-A(2A') relative stability remains nearly constant for all of the observed structural isomers. Alkyl substitution at the carbonyl carbon affects vibronic structure more profoundly than the energetics, while the converse is observed upon alkyl substitution at the alpha carbon.     

Stabilization of excess charge in isolated adenosine 5'-triphosphate and adenosine 5'-diphosphate multiply and singly charged anions

Multiply charged anions (MCAs) represent highly energetic species in the gas phase but can be stabilized through formation of molecular clusters with solvent molecules or counterions. We explore the intramolecular stabilization of excess negative charge in gas-phase MCAs by probing the intrinsic stability of the [adenosine 5'-triphosphate-2H](2-) ([ATP-2H](2-)), [adenosine 5'-diphosphate-2H](2-) ([ADP-2H](2-)), and H(3)P(3)O(10)(2-) dianions and their protonated monoanionic analogues. The relative activation barriers for decay of the dianions via electron detachment or ionic fragmentation are investigated using resonance excitation of ions isolated within a quadrupole trap. All of the dianions decayed via ionic fragmentation demonstrating that the repulsive Coulomb barriers (RCB) for ionic fragmentation lie below the RCBs for electron detachment. Both the electrospray ionization mass spectra (ESI-MS) and total fragmentation energies for [ATP-2H](2-), [ADP-2H](2-), and H(3)P(3)O(10)(2-) indicate that the multiply charged H(3)P(3)O(10)(2-) phosphate moiety is stabilized by the presence of the adenosine group and the stability of the dianions increases in the order H(3)P(3)O(10)(2-) < [ADP-2H](2-) < [ATP-2H](2-). Fully optimized, B3LYP/6-31+G* minimum energy structures illustrate that the excess charges in all of the phosphate anions are stabilized by intramolecular hydrogen bonding either within the phosphate chain or between the phosphate and the adenosine. We develop a model to illustrate that the relative magnitudes of the RCBs and hence the stability of these ions is dominated by the extent of intramolecular hydrogen bonding.     

Effect of cations of alkali metals and ammonium on the process of deposition and structure of iron-tungsten alloys

It is established that potassium ions facilitate expansion of the current density range where crystalline alloy deposits form. This is presumed to be connected with an increase in the hydrogen overvoltage, in connection with which alloy deposits turn amorphous at higher current densities and potentials corresponding to these, at which hydrogen evolution accelerates. A high alloy deposition rate and a sufficiently negative potential of its deposition are conditions not sufficient for transition from large-crystal to nanocrystalline and amorphous deposits. Here, a more important role is played by hydrogen that inserts itself into the crystal lattice. As one could assume, hydrogen in this case facilitates preservation of the emerging nonequilibrium structures, hindering crystallization processes as a result the iron hydride formation.     

Some observations on the relationship between charge and 13C chemical shift in cyclohexadienylic anions and cations

Carbon-13 chemical shifts δ^± in a variety of cyclohexadienylic cations and anions have been separated semi-empirically into contributions from (a) the hypothetical neutral framework, (b) charge effects and (c) interactions between ions and between ions and solvent molecules. Carbon-13 shifts for sites in neutral model compounds, δ⁰, approximate contribution (a) the shift differences for the model carbons δ^±_3,5-δ⁰_3,5 are assumed to reflect electric field effects (b). Thus what remains, δ^±_s-δ⁰_s- (δ^±_3,5-δ⁰_3,5) comes from the charge. The summation of these terms for each of the ions comes to ca. 165 ppm. This shows that a changein charge of ±1 of the neutral model, with correction for the electric field, brings about a change in shift of 165 ppm, thus supporting the linearity of charge with shift.     

Role of bridge energetics on the preference for hole or electron transfer leading to charge recombination in donor-bridge-acceptor molecules

The impact of donor-acceptor electronic coupling and bridge energetics on the preference for hole or electron transfer leading to charge recombination in a series of donor-bridge-acceptor (D-B-A) molecules was examined. In these systems, the donor is 3,5-dimethyl-4-(9-anthracenyl)-julolidine (DMJ-An) and acceptor is naphthalene-1,8:4,5-bis(dicarboximide) (NI), while the bridges are either oligo(p-phenyleneethynylene) (PE(n)P, where n = 1-3) 1-3 or oligo(2,7-fluorenone) (FN(n), where n = 1-3) 4-6. Photoexcitation of 1-3 and 4-6 produces DMJ(+?)-An-PE(n)P-NI(-?) and DMJ(+?)-An-FN(n)-NI(-?), respectively, which undergo radical pair intersystem crossing followed by charge recombination to yield both (3*)An and (3*)NI, which are observed by time-resolved electron paramagnetic resonance (TREPR) spectroscopy. (3*)NI is produced by hole transfer from DMJ(+?) to NI(-?), while (3*)An is produced by electron transfer from NI(-?) to DMJ(+?), using the agency of the bridge HOMOs and LUMOs, respectively. By monitoring the initial population of (3*)NI and (3*)An in 1-6, the data show that charge recombination occurs preferentially by selective hole transfer when the bridge is PE(n)P, while it occurs by preferential electron transfer when the bridge is FN(n). Over time, the initial population of (3*)NI decreases, while that of (3*)An increases, indicating that triplet-triplet energy transfer (TEnT) occurs. The observed distance dependence of TEnT from (3*)NI to An is weakly exponential with a decay parameter β = 0.08 ?(-1) for the PE(n)P series and β = 0.03 ?(-1) for the FN(n) series. In the PE(n)P series, this weak distance dependence is attributed to a transition from the superexchange regime to hopping transport as the energy gap for triplet energy injection onto the bridge becomes significantly smaller as n increases, while in the FN(n) series the corresponding energy gap is small for all n resulting in triplet energy transport by the hopping mechanism.     

Effects of fluorine on the structures and energetics of the propynyl and propargyl radicals and their anions

[reaction: see text] The adiabatic electron affinity (EA(ad)) of the CH(3)-C[triple bond]C(*) radical [experiment = 2.718 +/- 0.008 eV] and the gas-phase basicity of the CH(3)-C[triple bond]C:(-) anion [experiment = 373.4 +/- 2 kcal/mol] have been compared with those of their fluorine derivatives. The latter are studied using theoretical methods. It is found that there are large effects on the electron affinities and gas-phase basicities as the H atoms of the alpha-CH(3) group in the propynyl system are substituted by F atoms. The predicted electron affinities are 3.31 eV (FCH(2)-C[triple bond]C(*)), 3.86 eV (F(2)CH-C[triple bond]C(*)), and 4.24 eV (F(3)C-C[triple bond]C(*)), and the predicted gas-phase basicities of the fluorocarbanion derivatives are 366.4 kcal/mol (FCH(2)-C[triple bond]C:(-)), 356.6 kcal/mol (F(2)CH-C[triple bond]C:(-)), and 349.8 kcal/mol (F(3)C-C[triple bond]C:(-)). It is concluded that the electron affinities of fluoropropynyl radicals increase and the gas-phase basicities decrease as F atoms sequentially replace H atoms of the alpha-CH(3) in the propynyl system. The propargyl radicals, lower in energy than the isomeric propynyl radicals, are also examined and their electron affinities are predicted to be 0.98 eV ((*)CH(2)-C[triple bond]CH), 1.18 eV ((*)CFH-C[triple bond]CH), 1.32 eV ((*)CF(2)-C[triple bond] CH), 1.71 eV ((*)CH(2)-C[triple bond]CF), 2.05 eV ((*)CFH-C[triple bond]CF), and 2.23 eV ((*)CF(2)-C[triple bond]CF).     

Performance of ion chromatography in the determination of anions and cations in various natural waters with elevated mineralization

The performance of ion chromatography in the determination of anions and cations in natural mineral waters of different composition and different total mineralization was evaluated. Up to 12 ions of the 20 usually included in extended chemical analysis of natural waters were successfully determined by ion chromatography alone. At least 98.60% and up to 99.96% of total cation composition of mineral waters was determined by ion chromatography. Hydrogen carbonate predominated in anion composition of mineral waters and was determined titrimetrically. The percentage of anions determined by ion chromatography in the remaining anion composition of mineral waters was between 98.90% and 99.96%. The agreement between total concentrations of anions and cations in individual mineral waters determined predominantly by ion chromatography is very good and the performance of ion chromatography for the basic and for the extended chemical analysis of highly mineralized water samples is very high. Method development was assisted by previously developed algorithms and appropriate experimental conditions are also discussed.     

Effects of cations and anions of ionic liquids on the production of 5-hydroxymethylfurfural from fructose

Ionic liquids (ILs) with different cations and anions were used to study the effects on 5-hydroxymethylfurfural (HMF) preparation. It was found that both aggregations of cations and hydrogen bonds of anions with fructose played important roles. Molecular dynamics simulations were also performed to explain the experimental results.     

Adsorption of alkali metal cations and halide anions on metal oxides: prediction of Hofmeister series using 1-pK triple layer model

Adsorption of electrolyte ions on metal oxides significantly affects the interfacial charge distribution. The general procedure for the prediction of surface charge on oxides in salt solutions was given by Sverjensky for the 2-pK Triple Layer Model (2-pK TLM) (Sverjensky, Geochim. Cosmochim. Acta 69:225–257, 2005). Based on his parameters values and by assuming parameters transferability (Piasecki, J. Colloid Interface Sci. 302:389–395, 2006) we have predicted the adsorption constants for three monovalent ions (Rb⁺, F^?, Br^?) for eight oxides within the framework of the 1-pK Triple Layer Model (1-pK TLM). The obtained parameters values along with the previously reported ones (Piasecki, J. Colloid Interface Sci. 302:389–395, 2006) allowed us to compare the adsorption affinities of alkali metal cations and halide anions, and construct the following Hofmeister series for the cations (Cs⁺≈ Rb⁺≈ K⁺< Na⁺< Li⁺) and for the anions (F^?? Cl^?≈ Br^?< I^?) for investigated oxides. The same lyotropic series was predicted by the 2-pK TLM. It indicates that Hofmeister series is invariable during parameter transfer between surface complexation models.