Are radical cation states delocalized over GG and GGG hole traps in DNA?

Recently, Kurnikov et al. (J. Phys. Chem. B 2002, 106, 7) have shown that solvation of DNA duplexes destabilizes holes of sizes larger than three base pairs. In this paper, we consider the effects of solvation and internal reorganization on the hole charge distribution in sequences 5'-X-GG-Y-3'. Radical cation states in DNA are found to be localized to a single guanine site independent of the nature of adjacent base pairs.     

Electronic Structure and Catalysis on （001） Polar Surface of Cubic Zirconia

The electronic structure of (001) polar surface of cubic zirconia was studied by GGA(WC) approximation. We found the cubic lattice near (001) surface showed an intensive tendency to transfer to tetragonal lattice. The metallic state appeared on both the terminations. For O-termination, some O2p states were vacated and hole carriers concentrated on surface oxygen-ions. For Zr-ermination, some Zr4d states became partial occupied for the loss of O2p states. We observed the hole states were mainly localized at the corresponding ions on surface for both the terminations, while the charge states on Zr-termination were dispersed on surface.     

The key role of solvation dynamics in intramolecular electron transfer: time-resolved photophysics of crystal violet lactone

The intramolecular electron-transfer reaction in crystal violet lactone in polar aprotic solvents is studied with femtosecond transient absorption spectroscopy. The initially excited charge transfer state (1)CT A is rapidly converted into a highly polar charge transfer state (1)CT B. This ultrafast electron transfer is seen as a solvent-dependent dual fluorescence in steady-state spectra. We find that the electron-transfer process can be followed by a change from a double-peaked transient absorption spectrum to a single-peak one in the low picosecond range. The transient absorption kinetic curves are multiexponential, and the fitted time constants are solvent dependent but do not reproduce the known solvation times. For 6-dimethylaminophthalide, the optically active constituent of crystal violet lactone, only a small temporal evolution of the spectra is found. To explain these findings, we present a model that invokes a time-dependent electron-transfer rate. The rate is determined by the instantaneous separation of the two charge-transfer states. Because of their differing dipole moments, they are dynamically lowered to a different extent by the solvation. When they temporarily become isoenergetic, equal forward and backward transfer rates are reached. The intrinsic electron-transfer ( (1)CT A --> (1)CT B) reaction is probably as fast as that in the structurally analogous malachite green lactone (on the 100 fs time scale). The key element for the dynamics is therefore its control by the solvent, which changes the relative energetics of the two states during the solvation process. With further stabilization of the more polar state, the final equilibrium in state population is reached.     

On the relation between core electron binding energies of ions in solution and their solvation energies

Experimental and computational results from the study of positive and negative ions in solution are presented. The importance of short-range interactions between ion and solvent is studied with regard to core ionization of the ion. Exchange repulsion is found to be a significant factor in the interpretation of data for both cations and anions. Experimental results are presented for the core ionization of the OH^? ion in solution. The data show a strong similarity with corresponding data for the F^? ion, resulting in a large negative solvation energy for the final core hole state. The Be²⁺ ion shows large solvation energies for both ground- and core-ionized states, which is interpreted as due to charge transfer effects between solvent and ion.     

Charge asymmetries in hydration of polar solutes

We study the solvation of polar molecules in water. The center of water's dipole moment is offset from its steric center. In common water models, the Lennard-Jones center is closer to the negatively charged oxygen than to the positively charged hydrogens. This asymmetry of water's charge sites leads to different hydration free energies of positive versus negative ions of the same size. Here, we explore these hydration effects for some hypothetical neutral solutes, and two real solutes, with molecular dynamics simulations using several different water models. We find that, like ions, polar solutes are solvated differently in water depending on the sign of the partial charges. Solutes having a large negative charge balancing diffuse positive charges are preferentially solvated relative to those having a large positive charge balancing diffuse negative charges. Asymmetries in hydration free energies can be as large as 10 kcal/mol for neutral benzene-sized solutes. These asymmetries are mainly enthalpic, arising primarily from the first solvation shell water structure. Such effects are not readily captured by implicit solvent models, which respond symmetrically with respect to charge.     

Intramolecular Charge Transfer of Carotene‐porphyrin‐fullerene Triad: Sequential or Superexchange Cechanism

As an excellent artificial photosynthetic reaction center, the carotene (C)‐porphyrin (P)‐fullerene (F) triad was extensively investigated experimentally. To reveal the mechanism of the intramolecular charge transfer (ICT) on the mimic of photosynthetic solar energy conversion (such as singlet energy transfer between pigments, and photoinduced electron transfer from excited singlet states to give long‐lived charge‐separated states), the ICT mechanisms of C‐P‐F triad on the exciton were theoretically studied with quantum chemical methods as well as the 2D and 3D real space analysis approaches. The results of quantum chemical methods reveal that the excited states are the ICT states, since the densities of HOMO are localized in the carotene or porphyrin unit, and the densities of LUMO are localized in the fullerene unit. Furthermore, the excited states should be the intramolecular superexchange charge transfer (ISCT) states for the orbital transition from the HOMO whose densities are localized in the carotene to the LUMO whose densities are localized in the fullerene unit. The 3D charge difference densities can clearly show that some excited states are ISCT excited states, since the electron and hole are resident in the fullerene and carotene units, respectively. From the results of the electron‐hole coherence of the 2D transition density matrix, not only 3D results are supported, but also the delocalization size on the exciton can be observed. These phenomena were further interpreted with non‐linear optical effect. The large changes of the linear and non‐linear polarizabilities on the exciton result in the charge separate states, and if their changes are large enough, the ICT mechanism can become the ISCT on the exciton.     

Exploration of the secondary structure specific differential solvation dynamics between the native and molten globule states of the protein HP-36

Recent experiments have shown that the time dependence of fluorescence Stokes shift of a chromophore is substantially different when the chromophore is located in a molten globule (MG) state and in the native state of the same protein. To understand the origin of this difference, particularly the role of water in the differential solvation of the protein in the native and the MG states, we have carried out fully atomistic molecular dynamics simulations with explicit water of a partially unfolded MG state of the protein HP-36 and compared the results with the solvation dynamics of the protein in the folded native state. It is observed that the polar solvation dynamics of the three helical segments of the protein is influenced in a nonuniform heterogeneous manner in the MG state. While the equilibrium solvation time correlation function for helix-3 has been found to relax faster in the MG state as compared to that in the native state, the decay of the corresponding function for the other two helices slows down in the MG state. A careful analysis shows that the origin of such heterogeneous relative solvation behavior lies in the differential location of the polar probe residues and their exposure to bulk solvent. We find a significant negative cross-correlation between the contribution (to the solvation energy of a tagged amino acid residue) of water and the other groups of the protein, indicating a competing role in solvation. The sensitivity of solvation dynamics to the secondary structure and the immediate environment can be used to discriminate the partially unfolded and folded states. These results therefore should be useful in explaining recent solvation dynamics experiments on native and MG states of proteins.     

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.     

Influence of solvent on the energetics of hole transfer in DNA

We have investigated the contribution of molecular environment to the exchange reactions in the DNA molecule taking into account different geometries of the reaction centers in oxidized and reduced states. We have observed the influence of the ionization potential of the donor and the acceptor on the free energy of the hole transfer reaction in the solvated DNA molecule: A decrease of the free energy occurs if IPA > or = IPD and an increase if IPA < or = IPD. The corresponding decrease of the potential barrier by 0.244 eV for hole migration from (G-C) to (A-T) and increase for migration from (G-C) to (G-C)n in solvent have been determined. The prevalence of oxidation of the redox states in the molecule center in comparison to the molecule sides due to the nonuniform charge distribution along the phosphate backbone was found to be stronger for the non-neutralized backbone than for the neutralized case. The influence of the single counterion on the electrostatic interactions within the solute DNA molecule has been found to be smoothly spread over a long distance approximately 7-8 base pairs. Therefore, each counterion contributes to the oxidation potential of the 7-8 nearest nucleosides and any irregularity due to phosphate neutralization would not significantly modify the potential profile for the hole migration through the DNA molecule.     

Injection spectroscopy of localized states in thin insulating layers on semiconductor surfaces

An overview of charge injection techniques for studies of localized electron states in insulators is presented. These states control most important electrical properties of the materials, especially their thin layers and the multilayered structures containing them. Electronic properties of thin insulating layers are usually different from those of bulk material because in vicinity of an interface the thin film is subjected to action of structural strain, spatial confinement, extra energy release during growth or deposition, e.c. All these factors substantially affect the spectrum of localized electron states (intrinsic defects, dopants, impurities) and influence their spatial distribution. The interfaces often exhibit an unusual behaviour relative the defect generation and an impurity transport and segregation comparing with a bulk of insulator. The characterization of these states in thin-layered systems suffers from low sensitivity of both electron and optical spectroscopies to shallow electron states those have to be detected on the background of the signal from substrate. Nevertheless, the problem may be resolved by means of charge carrier injection into the insulating layer followed by monitoring of the charge becomes trapped. The localized states are detected by this way as a potential wells for the injected a mobile charge carriers. In thin layers the mean path of injected electron (hole) with respect to interaction with such a trap may greatly exceed thickness of the layer. In offers possibility to use linear modes for the trapping and detrapping analysis. We will show that under these conditions the charge-injection methods provide the most important phenomenological parameters of a localized state: the density per unit area, in-depth location, cross section for capture of carriers or recombination, energy position of the trapped carrier level in the insulator bandgap, e.c. On the base of these possibilities a non-destructive methods for characterization of extrinsic and intrinsic defects states are developed. Various charge injection and charge detection methods are compared. It shows unambiguously the advantages of using a semiconducting substrate for the insulator trapping studies. The limits of the linear models applicability are discussed in detail and the effects arising from the non-linear correlation phenomena are analyzed.     

Free energy landscape analysis of two-dimensional dipolar solvent model at temperatures below and above the rotational freezing point

Ionic solvation in a polar solvent is modeled by a central charge surrounded by dipolar molecules posted on two-dimensional distorted lattice sites with simple rotational dynamics. Density of states is calculated by applying the Wang-Landau algorithm to both the energy and polarization states. The free energy landscapes of solvent molecules as a function of polarization are depicted to explore the competition between the thermal fluctuation and solvation energy. Without a central charge, for temperatures higher than the energy scale of the dipole-dipole interactions, the energy landscape for the small polarization region exhibits a parabolic shape as predicted by Marcus [Rev. Mod. Phys. 65, 599 (1993)] for electron transfer reaction, while there is an additional quartic contribution to the landscape for the large polarization region. When the temperature drops, the simulated free energy landscapes are no longer smooth due to the presence of multiple local minima arising from the frustrated interaction among the dipoles. The parabolic contribution becomes negligible and the energy landscape becomes quartic in shape. For a strong central charge, the energy landscape exhibits an asymmetric profile due to the contributions of linear and cubic terms that arise from the charge-dipole interactions.     

A surface science approach to ultrafast electron transfer and solvation dynamics at interfaces

Excess electrons in polar media, such as water or ice, are screened by reorientation of the surrounding molecular dipoles. This process of electron solvation is of vital importance for various fields of physical chemistry and biology as, for instance, in electrochemistry or photosynthesis. Generation of such excess electrons in bulk water involves either photoionization of solvent molecules or doping with e.g. alkali atoms, involving possibly perturbing interactions of the system with the parent-cation. Such effects are avoided when using a surface science approach to electron solvation: in the case of polar adsorbate layers on metal surfaces, the substrate acts as an electron source from where photoexcited carriers are injected into the adlayer. Besides the investigation of electron solvation at such interfaces, this approach allows for the investigation of heterogeneous electron transfer, as the excited solvated electron population continuously decays back to the metal substrate. In this manner, electron transfer and solvation processes are intimately connected at any polar adsorbate-metal interface. In this tutorial review, we discuss recent experiments on the ultrafast dynamics of photoinduced electron transfer and solvation processes at amorphous ice-metal interfaces. Femtosecond time-resolved two-photon photoelectron spectroscopy is employed as a direct probe of the electron dynamics, which enables the analysis of all elementary processes: the charge injection across the interface, the subsequent electron localization and solvation, and the dynamics of electron transfer back to the substrate. Using surface science techniques to grow and characterize various well-defined ice structures, we gain detailed insight into the correlation between adsorbate structure and electron solvation dynamics, the location (bulk versus surface) of the solvation site, and the role of the electronic structure of the underlying metal substrate on the electron transfer rate.     

Photoelectron imaging of hydrated carbon dioxide cluster anions

The effects of homogeneous and heterogeneous solvation on the electronic structure and photodetachment dynamics of hydrated carbon dioxide cluster anions are investigated using negative-ion photoelectron imaging spectroscopy. The experiments are conducted on mass-selected [(CO(2))(n)()(H(2)O)(m)()](-) cluster anions with n and m ranging up to 12 and 6, respectively, for selected clusters. Homogeneous solvation in (CO(2))(n)()(-) has minimal effect on the photoelectron angular distributions, despite dimer-to-monomer anion core switching. Heterogeneous hydration, on the other hand, is found to have the marked effect of decreasing the photodetachment anisotropy. For example, in the [CO(2)(H(2)O)(m)()](-) cluster anion series, the photoelectron anisotropy parameter falls to essentially zero with as few as 5-6 water molecules. The analysis of the data, supported by theoretical modeling, reveals that in the ground electronic state of the hydrated clusters the excess electron is localized on CO(2), corresponding to a (CO(2))(n)()(-).(H(2)O)(m)() configuration for all cluster anions studied. The diminishing anisotropy in the photoelectron images of hydrated cluster anions is proposed to be attributable to photoinduced charge transfer to solvent, creating transient (CO(2))(n)().(H(2)O)(m)()(-) states that subsequently decay via autodetachment.     

Base sequence effects on transport in DNA

Given the success of the polaron model based on solvation in accounting for the width of a hole polaron on an all-adenine (A) sequence on DNA, we extend the calculations to other sequences. We find excellent agreement with the free energy differences measured by Lewis et al. (J. Am. Chem. Soc. 2000, 122, 12037-12038) between a guanine (G) cation and a pair of bases, GG, or a triple of bases, GGG, in all cases surrounded by As, by treating AGGA and AGGGA as solvated polarons. There is additional support for hole polaron formation in DNA from experiments in which oxidative damage due to injected holes is investigated in sequences involving Gs and As. Theory and comparison with transport measurements on repeated sequences involving multiple thymines (Ts) or combinations such as ATs or GCs, where C is cytosine, led to the suggestion that the basic sequences in these cases must be polarons whose wave functions have substantial amplitudes on both chains in a duplex. The size of an electron polaron in DNA is predicted to be similar to that of a hole polaron, approximately 4 or 5 bases. Although experiments have shown that polaron hopping is the dominant mode of charge transport in DNA with repeated sequences such as AGGA, further investigations, particularly of temperature dependence of site energies and transfer integrals, are needed to determine to what extent hole transport takes place by polaron hopping for arbitrary DNA sequences.     

Structure of triplex DNA in the gas phase

Extensive (more than 90 microseconds) molecular dynamics simulations complemented with ion-mobility mass spectrometry experiments have been used to characterize the conformational ensemble of DNA triplexes in the gas phase. Our results suggest that the ensemble of DNA triplex structures in the gas phase is well-defined over the experimental time scale, with the three strands tightly bound, and for the most abundant charge states it samples conformations only slightly more compact than the solution structure. The degree of structural alteration is however very significant, mimicking that found in duplex and much larger than that suggested for G-quadruplexes. Our data strongly supports that the gas phase triplex maintains an excellent memory of the solution structure, well-preserved helicity, and a significant number of native contacts. Once again, a linear, flexible, and charged polymer as DNA surprises us for its ability to retain three-dimensional structure in the absence of solvent. Results argue against the generally assumed roles of the different physical interactions (solvent screening of phosphate repulsion, hydrophobic effect, and solvation of accessible polar groups) in modulating the stability of DNA structures.     

Solvent Effects on Ultrafast Charge Transfer Population: Insights from the Quantum Dynamics of Guanine-Cytosine in Chloroform

We study the ultrafast photoactivated dynamics of the hydrogen bonded dimer Guanine-Cytosine in chloroform solution, focusing on the population of the Guanine→Cytosine charge transfer state (GC-CT), an important elementary process for the photophysics and photochemistry of nucleic acids. We integrate a quantum dynamics propagation scheme, based on a linear vibronic model parameterized through time dependent density functional theory calculations, with four different solvation models, either implicit or explicit. On average, after 50 fs, 30∼40 % of the bright excited state population has been transferred to GC-CT. This process is thus fast and effective, especially when transferring from the Guanine bright excited states, in line with the available experimental studies. Independent of the adopted solvation model, the population of GC-CT is however disfavoured in solution with respect to the gas phase. We show that dynamical solvation effects are responsible for this puzzling result and assess the different chemical-physical effects modulating the population of CT states on the ultrafast time-scale. We also propose some simple analyses to predict how solvent can affect the population transfer between bright and CT states, showing that the effect of the solute/solvent electrostatic interactions on the energy of the CT state can provide a rather reliable indication of its possible population.     

Carbonyl Charge Solvation Patterns May Relate to Fragmentation Classes in Collision-Activated Dissociation

Here, we investigate the hypothesis that the origin of Class I fragmentation in tryptic peptide dications corresponding to the cleavage of the first two amino acids from the N-terminus is due to a dominant charge solvation pattern. Molecular dynamics simulations (MDS) of model A(n)R dications confirmed the existence of a persistent solvation of the protonated N-terminus on the second backbone carbonyl. Additionally, MDS predicted a new distinct fragmentation class corresponding to the loss of two amino acids from the C-terminus. This prediction was confirmed experimentally at very low excitation levels. The pattern produced by electron transfer dissociation of the same dications gave markedly decreased cleavage frequencies at the second peptide bond, which, within the non-local fragmentation mechanism, supports the preferential charge solvation on the second carbonyl. Taken together, these results confirm the role of a charge solvation pattern in the origin of fragmentation classes.     

Elucidation of the thermochemical properties of triphenyl- or tributyl-substituted Si-, Ge-, and Sn-centered radicals by means of electrochemical approaches and computations

Redox potentials of a number of triphenyl- or tributyl-substituted Si-, Ge-, or Sn-centered radicals, R(3)M(*), have been measured in acetonitrile, tetrahydrofuran, or dimethyl sulfoxide by photomodulated voltammetry or through a study of the oxidation process of the corresponding anions in linear sweep voltammetry. For the results pertaining to the Ph(3)M(*) series (including literature data for M = C), the order of reduction potentials follows Sn > Ge > C > Si, while for the two oxidation potentials, it is C > Si. The effect of the R group on the redox properties of R(3)Sn(*) is pronounced in that the reduction potential is more negative by 490 mV in tetrahydrofuran (390 mV in dimethyl sulfoxide) when R is a butyl rather than a phenyl group. The experimental trends have been substantiated through quantum chemical calculations, and they can be explained qualitatively by considering a combination of effects, such as charge capacity being most pronounced for the heavier elements, resonance stabilization present for the planar Ph(3)C(*) and all R(3)M(+)(), and finally a contribution from solvation. The solvation of R(3)M(-) is observed to be relatively strong because of a rather localized negative charge in the pyramidal geometry. However, there is no evidence in the calculations to support the existence of covalent interactions between solvent and anions. The solvation of R(3)M(+)() is relatively weak, which may be attributed to the planar geometry around the center atom, leading to more spread out charge than that for a pyramidal geometry. Although the calculated solvation energies based on the polarizable continuum model approach exhibit the expected trends, they are not able to reproduce the experimentally derived values on a detailed level for these types of ions. An evaluation of the general performance of the continuum model is provided on the basis of present and previous studies.