Strong localization of positive charge in DNA induced by its interaction with environment

We investigate a quantum state of positive charge in DNA. A quantum state of electron hole is determined by the competition of the pi-stacking interaction b sharing a charge between different base pairs and the interaction lambda with the local environment which attempts to trap charge. To determine which interaction dominates, we investigate charge quantum states in various (GC)(n) sequences choosing DNA parameters that satisfy experimental data for the balance of charge transfer rates G(+) <--> G(n)(+), n = 2, 3. We show that experimental data can be consistent with theory only assuming b G(n)(+), n > or = 4 and comparing the experimental results with our predictions.     

Free energy gap laws for the pulse-induced and stationary fluorescence quenching by reversible charge transfer in polar solutions

The Stern-Volmer constants for either pulse-induced or stationary fluorescence being quenched by a contact charge transfer are calculated and their free energy dependencies (the free energy gap laws) are specified. The reversibility of charge transfer is taken into account as well as spin conversion in radical ion pairs, followed by their recombination in either singlet or triplet neutral products. The natural decay of triplets as well as their impurity quenching by ionization are accounted for when estimating the fluorescence quantum yield and its free energy dependence.     

Elementary steps for charge transport in DNA: thermal activation vs. tunneling

Using stacks of Watson–Crick base pairs as an important example of multichromophoric molecular assemblies, we studied charge migration in DNA with special emphasis on the mechanism of hole hopping between neighboring guanines (G) connected by the adenine–thymine (AT) bridge. The tight-binding model proposed for this elementary step shows that for short AT bridges, hole transfer between two G bases proceeds via quantum mechanical tunneling. By contrast, hopping over long bridges requires thermal activation. The condition for crossover between tunneling and thermal activation near room temperature is specified and applies to the analysis of experimental data. We show that thermal activation dominates, if the bridge between two G bases contains more than three AT pairs. Our theoretical findings predict that the replacement of AT base pairs by GC pairs increases the efficiency of hole transport only in the case of short base pair sequences. For long sequences, however, the opposite effect is expected.     

Electron transfer dissociation versus collisionally activated dissociation of cationized biodegradable polyesters

Biodegradable polyesters were ionized by electrospray ionization and characterized by tandem mass spectrometry using collisionally activated dissociation (CAD) and electron transfer dissociation (ETD) as activation methods. The compounds studied include one homopolymer, polylactide and two copolymers, poly(ethylene adipate) and poly(butylene adipate). CAD of [M+2Na]²⁺ ions from these polyesters proceeds via charge‐remote 1,5‐H rearrangements over the ester groups, leading to cleavages at the (CO)O–alkyl bonds. ETD of the same precursor ions creates a radical anion at the site of electron attachment, which fragments by radical‐induced cleavage of the (CO)O–alkyl bonds and by intramolecular nucleophilic substitution at the (CO)–O bonds. In contrast to CAD, ETD produces fragments in one charge state only and does not cause consecutive fragmentations, which simplifies spectral interpretation and permits conclusive identification of the correct end groups. The radical‐site reactions occurring during ETD are very similar with those reported for ETD of protonated peptides. Unlike multiply protonated species, multiply sodiated precursors form ion pairs (salt bridges) after electron transfer, thereby promoting dissociations via nucleophilic displacement in addition to the radical‐site dissociations typical in ETD. Copyright © 2012 John Wiley & Sons, Ltd.     

Crossover from superexchange to hopping as the mechanism for photoinduced charge transfer in DNA hairpin conjugates

The mechanism and dynamics of photoinduced charge separation and charge recombination have been investigated in synthetic DNA hairpins possessing donor and acceptor stilbenes separated by one to seven A:T base pairs. The application of femtosecond broadband pump-probe spectroscopy, nanosecond transient absorption spectroscopy, and picosecond fluorescence decay measurements permits detailed analysis of the formation and decay of the stilbene acceptor singlet state and of the charge-separated intermediates. When the donor and acceptor are separated by a single A:T base pair, charge separation occurs via a single-step superexchange mechanism. However, when the donor and acceptor are separated by two or more A:T base pairs, charge separation occurs via a multistep process consisting of hole injection, hole transport, and hole trapping. In such cases, hole arrival at the electron donor is slower than hole injection into the bridging A-tract. Rate constants for charge separation (hole arrival) and charge recombination are dependent upon the donor-acceptor distance; however, the rate constant for hole injection is independent of the donor-acceptor distance. The observation of crossover from a superexchange to a hopping mechanism provides a "missing link" in the analysis of DNA electron transfer and requires reevaluation of the existing literature for photoinduced electron transfer in DNA.     

Femtosecond-Picosecond Laser Photolysis Studies on Photoinduced Electron Transfer Phenomena in Solutions

Results of our femtosecond-picosecond laser photolysis studies on photoinduced electron transfer phenomena in solutions including exciplex dynamics and its solvent dependences, energy gap dependences of photoinduced charge separation and charge recombination of various geminate ion pairs, mechanisms of chemical reactions via exciplexes and ion pairs, dynamics of photoinduced election transfer in hydrogen bonding complexes, dynamics and mechanisms of photoinduced electron transfer in fixed distance donor acceptor dyads and photosynthetic reaction center models, and mechanisms of electron ejection from solute fluorescent state in polar solutions are summarized and discussed.     

Photoinduced ultrafast electron transfer from CdSe quantum dots to Re-bipyridyl complexes

Ultrafast dissociation of excitons in CdSe quantum dots via electron transfer to adsorbed Re-bipyridyl complexes was demonstrated. The dissociation pathway was determined by the observation of reduced adsorbate using femtosecond IR spectroscopy. The rate of electron transfer was shown to increase at smaller QD sizes. Electron transfer time as fast as 2.3 ps was observed, faster than the exciton annihilation time in CdSe. The ultrafast charge separation in this quantum dot-adsorbate donor-acceptor complex provides a potential approach for separating multiple excitons in quantum dots.     

Nonadiabatic time-dependent wave packet study of the D+ + H2 reaction system

A theoretical investigation on the nonadiabatic processes of the D(+) + H(2) reaction system has been carried out by means of exact three-dimensional nonadiabatic time-dependent wave packet calculations with an extended split operator scheme (XSOS). The diabatic potential energy surface newly constructed by Kamisaka et al. (J. Chem. Phys. 2002, 116, 654) was employed in the calculations. This study provided quantum cross sections for three competing channels of the reactive charge transfer, the nonreactive charge transfer, and the reactive noncharge transfer, which contrasted markedly to many previous quantum theoretical reports on the (DH(2))(+) system restricted to the total angular momentum J = 0. These quantum theoretical cross sections derived from the ground rovibrational state of H(2) show wiggling structures and an increasing trend for both the reactive charge transfer and the nonreactive charge transfer but a decreasing trend for the reactive noncharge transfer throughout the investigated collision energy range 1.7-2.5 eV. The results also show that the channel of the reactive noncharge transfer with the largest cross section is the dominant one. A further investigation of the v-dependent behavior of the probabilities for the three channels revealed an interesting dominant trend for the reactive charge transfer and the nonreactive charge transfer at vibrational excitation v = 4 of H(2). In addition, the comparison between the centrifugal sudden (CS) and exact calculations showed the importance of the Coriolis coupling for the reactive system. The computed quantum cross sections are also compared with the experimental measurement results.     

Molecular origin of differences in hole and electron mobility in amorphous Alq3--a multiscale simulation study

In order to determine the molecular origin of the difference in electron and hole mobilities of amorphous thin films of Alq(3) (meridional Alq(3) (tris(8-hydroxyquinoline) aluminium)) we performed multiscale simulations covering quantum mechanics, molecular mechanics and lattice models. The study includes realistic disordered morphologies, polarized site energies to describe diagonal disorder, quantum chemically calculated transfer integrals for the off-diagonal disorder, inner sphere reorganization energies and an approximative scheme for outer sphere reorganization energies. Intermolecular transfer rates were calculated via Marcus-theory and mobilities were simulated via kinetic Monte Carlo simulations and by a Master Equation approach. The difference in electron and hole mobility originates from the different localization of charge density in the radical anion (more delocalized) compared to the radical cation (more confined). This results in higher diagonal disorder for holes and less favourable overlap properties for the hole transfer integrals leading to an overall higher electron mobility.     

Effects of KI encapsulation in single-walled carbon nanotubes by Raman and optical absorption spectroscopy

The effect of KI encapsulation in narrow (HiPCO) single-walled carbon nanotubes is studied via Raman spectroscopy and optical absorption. The analysis of the data explores the interplay between strain and structural modifications, bond-length changes, charge transfer, and electronic density of states. KI encapsulation appears to be consistent with both charge transfer and strain that shrink both the C-C bonds and the overall nanotube along the axial direction. The charge transfer in larger semiconducting nanotubes is low and comparable with some cases of electrochemical doping, while optical transitions between pairs of singularities of the density of states are quenched for narrow metallic nanotubes. Stronger changes in the density of states occur in some energy ranges and are attributed to polarization van der Waals interactions caused by the ionic encapsulate. Unlike doping with other species, such as atoms and small molecules, encapsulation of inorganic compounds via the molten-phase route provides stable effects due to maximal occupation of the nanotube inner space.     

Constraints in post-synthesis ligand exchange for hybrid organic (MEH-PPV)–inorganic (CdSe) nanocomposites

For an optimum charge/energy transfer performance of hybrid organic–inorganic colloidal nanocrystals for applications such as photonic devices and solar cells, the determining factors are the distance between the nanocrystal and polymer which greatly depends upon nanocrystal size/nanocrystal ligands. Short chain ligands are preferred to ensure a close contact between the donor and acceptor as a result of the tunnelling probability of the charges and the insulating nature of long alkyl chain molecules. Short distances increase the probability for tunnelling to occur as compared to long distances induced by long alkyl chains of bulky ligands which inhibit tunnelling altogether. The ligands on the as-synthesized nanocrystals can be exchanged for various other ligands to achieve desirable charge/energy transfer properties depending on the bond strength of the ligand on the nanocrystal compared to the replacement ligand. In this work, the constraints involved in post-synthesis ligand exchange process have been evaluated, and these factors have been tuned via wet chemistry to tailor the hybrid material properties via appropriate selection of the nanocrystal capping ligands. It has been found that both oleic acid and oleylamine (OLA)-capped cadmium selenide (CdSe) quantum dots (QDs) as compared with trioctylphosphine oxide (TOPO)-passivated CdSe QDs are of high quality, and they provide better steric stability against coagulation, homogeneity, and photostability to their respective polymer:CdSe nanocomposites. CdSe QDs particularly with OLA capping have relatively smaller surface energies, and thus, lesser quenching capabilities show dominance of photoinduced Forster energy transfer between donors (polymer) and acceptors (CdSe nanocrystals) as compared to charge transfer mechanism as observed in polymer:CdSe (TOPO) composites. It is conjectured that size quantization effects, stereochemical compatibility of ligands (TOPO, oleic acid, and oleyl amine), and polymer MEH-PPV stability greatly influence the photophysics and photochemistry of hybrid polymer–semiconductor nanocomposites.     

Homopairing possibilities of the DNA base adenine

Using calculations based on the ab initio density functional theory, we for the first time report all possible planar DNA base adenine homodimers. Two density functionals and both localized and plane wave basis sets were used, and the results are compared with previous quantum chemical and semiempirical calculations available for a few pairs. We find that there are 21 possible planar adenine pairs with variable binding energies ranging from -0.03 to -0.86 eV. More stable pairs are associated with two strong hydrogen bonds formed between the monomers, while the least stable pairs are characterized by two or one relatively weak bonds. We find that stable hydrogen bonds can be characterized by the difference charge density that shows well-developed regions of alternating excess and depletion of the electron charge similar to a "kebab" structure. The presented detailed information on all planar adenine pairs can be utilized, for example, in considering possible adenine monolayers seen on various surfaces.     

Electronic coupling mediated by stacked [Thymine-Hg-Thymine] base pairs

Very recently it has been shown that stable metal-mediated base pairs [Thymine-Hg-Thymine] can form in DNA. To estimate the effect of such pairs on the efficiency of charge transfer through DNA, we carry out quantum mechanical calculations of double-stranded pi-stacks GXG, GXXG, and GXXXG, where X = [Thymine-Hg-Thymine] and stacks GT(n)G of canonical base pairs. The charge-transfer efficiency in short duplexes GXG and GTG is found to be similar. However, the donor-acceptor coupling in GXXG and GXXXG is stronger by a factor of 2.5-3.0 than that in GT(n)G (n = 2 and 3), respectively. It is shown that the valence orbitals of Hg atoms do not essentially participate in mediating the electronic coupling for hole transfer; however, they may play an important role in excess electron transfer.     

Protonation of the chromophore in the photoactive yellow protein

The photoactive yellow protein (PYP) acts as a light sensor to its bacterial host: it responds to light by changing shape. After excitation by blue light, PYP undergoes several transformations, to partially unfold into its signaling state. One of the crucial steps in this photocycle is the protonation of p-coumaric acid after excitation and isomerization of this chromophore. Experimentalists still debate on the nature of the proton donor and on whether it donates the hydrogen directly or indirectly. To obtain better knowledge of the mechanism, we studied this proton transfer using Car-Parrinello molecular dynamics, classical molecular dynamics, and computer simulations combining these two methods (quantum mechanics/molecular mechanics, QMMM). The simulations reproduce the chromophore structure and hydrogen-bond network of the protein measured by X-ray crystallography and NMR. When the chromophore is protonated, it leaves the assumed proton donor, glutamic acid 46, with a negative charge in a hydrophobic environment. We show that the stabilization of this charge is a very important factor in the mechanism of protonation. Protonation frequently occurs in simplified ab initio simulations of the chromophore binding pocket in vacuum, where amino acids can easily hydrogen bond to Glu46. When the complete protein environment is incorporated in a QMMM simulation on the complete protein, no proton transfer is observed within 14 ps. The hydrogen-bond rearrangements in this time span are not sufficient to stabilize the new protonation state. Force field molecular dynamics simulations on a much longer time scale have shown which internal rearrangements of the protein are needed. Combining these simulations with more QMMM calculations enabled us to check the stability of protonation states and clarify the initial requirements for the proton transfer in PYP.     

Electron transfer in quantum-dot-sensitized ZnO nanowires: ultrafast time-resolved absorption and terahertz study

Photoinduced electron injection dynamics from CdSe quantum dots to ZnO nanowires is studied by transient absorption and time-resolved terahertz spectroscopy measurements. Ultrafast electron transfer from the CdSe quantum dots to ZnO is proven to be efficient already on a picoseconds time scale (τ = 3-12 ps). The measured kinetics was found to have a two-component character, whose origin is discussed in detail. The obtained results suggest that electrons are injected into ZnO via an intermediate charge transfer state.     

Charge carrier photogeneration in polymers

The charge carrier photogeneration in polymers can be depicted as a multistage process that involves i) photoexcitation to a neutral molecular electronic state, ii) autoionization of the excited state, iii) thermalization of the hot electron, leading to the formation of a Coulomb field-bound geminate electron-hole pair, and iv) thermal dissociation of the electron-hole pair into free carriers. This model is proposed for all types of polymers with a large ocnjugated pendant group and both the saturated and non-saturated main chain. The separation distance of the electron-hole pairs ranges from 2 to 3 nm, and the primary quantum efficiency of the electron-hole pairs formation assumes values of several tenths of charge per photon. In intrinsic materials like substituted polyacetylenes both the interchain and intrachain charge transfer excitons can be formed. Onsager's theory can provide a satisfactory explanation of the dissociation step. In polymers with the saturated main chain and large conjugated pendant groups the charge-transfer excitons are very often stabilized by self-trapping in dimer deep traps. Dedicated to Prof. Dr. W. Pechhold on the occasion of his 60th birthday     

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.     

Synthesis and photoinduced electron transfer processes of rotaxanes bearing [60]fullerene and zinc porphyrin: effects of interlocked structure and length of axle with porphyrins

Three rotaxanes, with axles with two zinc porphyrins (ZnPs) at both ends penetrating into a necklace pending a C60 moiety, were synthesized with varying interlocked structures and axle lengths. The intra-rotaxane photoinduced electron transfer processes between the spatially positioned C60 and ZnP in rotaxanes were investigated. Charge-separated (CS) states (ZnP*+, C60*-)rotaxane are formed via the excited singlet state of ZnP (1ZnP*) to the C60 moiety in solvents such as benzonitrile, THF, and toluene. The rate constants and quantum yields of charge separation via 1ZnP decrease with axle length, but they are insensitive to solvent polarity. When the axle becomes long, charge separation takes place via the excited triplet state of ZnP (3ZnP*). The lifetime of the CS state increases with axle length from 180 to 650 ns at room temperature. The small activation energies of charge recombination were evaluated by temperature dependence of electron-transfer rate constants, probably reflecting through-space electron transfer in the rotaxane structures.     

Long-distance radical cation migration in duplex DNA: the effect of contiguous A.A and T.T mismatches on efficiency and mechanism

A series of DNA oligomers was prepared. Each oligomer contained an anthraquinone group (AQ, sensitizer) covalently linked at a 5'-end and two GG steps that surrounded a variable region. The variable region was composed of A.T base pairs or A.A or T.T mismatches. Irradiation of the AQ injected a radical cation (hole) into the DNA that migrated through the duplex, being trapped by reaction with H2O of O2 at the GG steps. The effect of substituting A.A or T.T mismatches for Watson-Crick base pairs was examined. For A.A mispairs, charge transfer through the mismatch region was as efficient as through normal DNA. For the T.T mismatches, radical cation transport was strongly distance-dependent. These findings suggest that A.A mismatches form a zipper-like motif, and charge transport proceeds by a hopping mechanism. In contrast, charge transport through the T.T mismatches (where there are no purines) may proceed by quantum mechanical tunneling.