Estimates of electronic coupling for excess electron transfer in DNA

Electronic coupling Vda is one of the key parameters that determine the rate of charge transfer through DNA. While there have been several computational studies of Vda for hole transfer, estimates of electronic couplings for excess electron transfer (ET) in DNA remain unavailable. In the paper, an efficient strategy is established for calculating the ET matrix elements between base pairs in a π stack. Two approaches are considered. First, we employ the diabatic-state (DS) method in which donor and acceptor are represented with radical anions of the canonical base pairs adenine-thymine (AT) and guanine-cytosine (GC). In this approach, similar values of Vda are obtained with the standard 6-31 G* and extended 6-31++ G* basis sets. Second, the electronic couplings are derived from lowest unoccupied molecular orbitals (LUMOs) of neutral systems by using the generalized Mulliken-Hush or fragment charge methods. Because the radical-anion states of AT and GC are well reproduced by LUMOs of the neutral base pairs calculated without diffuse functions, the estimated values of Vda are in good agreement with the couplings obtained for radical-anion states using the DS method. However, when the calculation of a neutral stack is carried out with diffuse functions, LUMOs of the system exhibit the dipole-bound character and cannot be used for estimating electronic couplings. Our calculations suggest that the ET matrix elements Vda for models containing intrastrand thymine and cytosine bases are essentially larger than the couplings in complexes with interstrand pyrimidine bases. The matrix elements for excess electron transfer are found to be considerably smaller than the corresponding values for hole transfer and to be very responsive to structural changes in a DNA stack

Transferència d’electrò i protó als intermediaris de reacció de les hemo-catalases

Projecte de recerca elaborat a partir d’una estada a l’University of Pennsylvania, EUA, entre els mesos d’agosta a desembre del 2006. Les hemo-catalases són enzims que protegeixen les cèl•lules dels efectes tòxics del peròxid d'hidrogen. Aquesta reacció té lloc en dues etapes, via l'intermediari Compost I (Cpd I). Tanmateix, el Compost I pot seguir una reacció secundària, a través de l'intermediari Compost II. Hi ha dos tipus d'hemo-catalases: les hemo-b (com la d'Helicobacter pylori, HPC) i les hemo-d catalases (com la de Penicillium vitale, PVC). Experimentalment s'observa que les hemo-b catalases formen Cpd II més fàcilment que les hemo-d. La formació del Cpd II consta de dos processos: la reducció del catió radical porfirínic i la protonació del grup oxoferril. Durant l'estada, es va estudiar el procès de transferència electrònica a la porfirina utilitzant una metodologia desenvolupada recentment. Els resultats mostren que per PVC la reducció és més fàcil que per HPC. Posteriorment hem realitzat una sèrie de optimitzacions de geometria CPMD QM/MM al llarg del camí per la transferència de protó (PT) de la histidina distal a l'oxoferril. Mentre que per HPC aquesta PT és espontània, per PVC l'isòmer hidroxoferrílic és menys estable que el catió imidazoli.

Electrochemically promoted carbon-halide bond cleavage in 4-nitrobenzyl halides

This manuscript reports the study of the carbon-halide bond cleavage in 4-nitrobenzyl halides, taking special attention to the iodide and fluoride derivatives. The electrochemical reduction mechanism has been disclosed for both compounds by terms of cyclic voltammetry and controlled potential electrolysis. In the case of 4-nitrobenzyl iodide, a first one electron irreversible wave leads to the corresponding 4-nitrobenzyl radical and iodide. However, in the case of 4-nitrobenzyl fluoride, a first one-electron reversible wave appears at –1.02 vs. SCE followed by one electron irreversible wave. In this second electron transfer process, the cleavage of the C-F bond is taking place, so the bond cleavage reaction occurs at the dianion level. To disclose and understand the electrochemical reduction mechanisms that allows to obtain important thermodynamic and kinetic data that would help in the understanding of C-X bond cleavage. This type of bond dissociation reactions are involved in the metabolism pathways of the human body.

Triggering the generation of an iron(IV)-oxo compound and its reactivity toward sulfides by RuII photocatalysis

The preparation of [FeIV(O)(MePy2tacn)]2+ (2, MePy2tacn = N-methyl-N,N-bis(2-picolyl)-1,4,7-triazacyclononane) by reaction of [FeII(MePy2tacn)(solvent)]2+ (1) and PhIO in CH3CN and its full characterization are described. This compound can also be prepared photochemically from its iron(II) precursor by irradiation at 447 nm in the presence of catalytic amounts of [Ru II(bpy)3]2+ as photosensitizer and a sacrificial electron acceptor (Na2S2O8). Remarkably, the rate of the reaction of the photochemically prepared compound 2 toward sulfides increases 150-fold under irradiation, and 2 is partially regenerated after the sulfide has been consumed; hence, the process can be repeated several times. The origin of this rate enhancement has been established by studying the reaction of chemically generated compound 2 with sulfides under different conditions, which demonstrated that both light and [Ru II(bpy)3]2+ are necessary for the observed increase in the reaction rate. A combination of nanosecond time-resolved absorption spectroscopy with laser pulse excitation and other mechanistic studies has led to the conclusion that an electron transfer mechanism is the most plausible explanation for the observed rate enhancement. According to this mechanism, the in-situ-generated [RuIII(bpy)3] 3+ oxidizes the sulfide to form the corresponding radical cation, which is eventually oxidized by 2 to the corresponding sulfoxide

Electronic couplings and on-site energies for hole transfer in DNA: systematic quantum mechanical/molecular dynamic study

The electron hole transfer (HT) properties of DNA are substantially affected by thermal fluctuations of the π stack structure. Depending on the mutual position of neighboring nucleobases, electronic coupling V may change by several orders of magnitude. In the present paper, we report the results of systematic QM/molecular dynamic (MD) calculations of the electronic couplings and on-site energies for the hole transfer. Based on 15 ns MD trajectories for several DNA oligomers, we calculate the average coupling squares 〈 V2 〉 and the energies of basepair triplets X G+ Y and X A+ Y, where X, Y=G, A, T, and C. For each of the 32 systems, 15 000 conformations separated by 1 ps are considered. The three-state generalized Mulliken-Hush method is used to derive electronic couplings for HT between neighboring basepairs. The adiabatic energies and dipole moment matrix elements are computed within the INDO/S method. We compare the rms values of V with the couplings estimated for the idealized B -DNA structure and show that in several important cases the couplings calculated for the idealized B -DNA structure are considerably underestimated. The rms values for intrastrand couplings G-G, A-A, G-A, and A-G are found to be similar, ∼0.07 eV, while the interstrand couplings are quite different. The energies of hole states G+ and A+ in the stack depend on the nature of the neighboring pairs. The X G+ Y are by 0.5 eV more stable than X A+ Y. The thermal fluctuations of the DNA structure facilitate the HT process from guanine to adenine. The tabulated couplings and on-site energies can be used as reference parameters in theoretical and computational studies of HT processes in DNA

Energy transfer mechanism and Auger effect in Er3+ coupled silicon nanoparticle samples

We report a spectroscopic study about the energy transfer mechanism among silicon nanoparticles (Si-np), both amorphous and crystalline, and Er ions in a silicon dioxide matrix. From infrared spectroscopic analysis, we have determined that the physics of the transfer mechanism does not depend on the Si-np nature, finding a fast (< 200 ns) energy transfer in both cases, while the amorphous nanoclusters reveal a larger transfer efficiency than the nanocrystals. Moreover, the detailed spectroscopic results in the visible range here reported are essential to understand the physics behind the sensitization effect, whose knowledge assumes a crucial role to enhance the transfer rate and possibly employing the material in optical amplifier devices. Joining the experimental data, performed with pulsed and continuous-wave excitation, we develop a model in which the internal intraband recombination within Si-np is competitive with the transfer process via an Auger electron"recycling" effect. Posing a different light on some detrimental mechanism such as Auger processes, our findings clearly recast the role of Si-np in the sensitization scheme, where they are able to excite very efficiently ions in close proximity to their surface. (C) 2010 American Institute of Physics.

Design of electron band pass filters for electrically biased finite superlattices

We design optimal band pass filters for electrons in semiconductor heterostructures, under a uniform applied electric field. The inner cells are chosen to provide a desired transmission window. The outer cells are then designed to transform purely incoming or outgoing waves into Bloch states of the inner cells. The transfer matrix is interpreted as a conformal mapping in the complex plane, which allows us to write constraints on the outer cell parameters, from which physically useful values can be obtained.

Thermal and back-action noises in dual-sphere gravitational-wave detectors

We study the sensitivity limits of a broadband gravitational-wave detector based on dual resonators such as nested spheres. We determine both the thermal and back-action noises when the resonators displacements are read out with an optomechanical sensor. We analyze the contributions of all mechanical modes, using a new method to deal with the force-displacement transfer functions in the intermediate frequency domain between the two gravitational-wave sensitive modes associated with each resonator. This method gives an accurate estimate of the mechanical response, together with an evaluation of the estimate error. We show that very high sensitivities can be reached on a wide frequency band for realistic parameters in the case of a dual-sphere detector.

Polyconductivity in polypyrrole: the correlated electron glass

p-toluensulfonate doped polypyrrole ~PPy!, undergoes an electric-field induced reversible transition from an insulating state to a highly conductive one. The spatially average field can be as small as 200 V/cm, when the temperature of the sample is below 20 K. The applied electric field leads to a sharp jump in the value of the current to a value which is nearly five orders of magnitude higher than before. When the applied electric field is reduced to below a critical value, the system switches back to a low conductive state. The effect is reversible, symmetric in voltage, and reproducible for different samples. The switching is, we believe, an electronic glass melting transition and it is due to the disordered, highly charged granular nature of PPy.

Polyconductivity in polypyrrole: The correlated electron gas

p-toluensulfonate doped polypyrrole (PPy), undergoes an electric-field induced reversible transition from an insulating state to a highly conductive one. The spatially average field can be as small as 200 V/cm, when the temperature of the sample is below 20 K. The applied electric field leads to a sharp jump in the value of the current to a value which is nearly five orders of magnitude higher than before. When the applied electric field is reduced to below a critical value, the system switches back to a low conductive state. The effect is reversible, symmetric in voltage, and reproducible for different samples. The switching is, we believe, an electronic glass melting transition and it is due to the disordered, highly charged granular nature of PPy.

Technology transfer at the periphery of the Mycenaean world: the cases of Mycenaean pottery found in central Macedonia (Greece) and the Plain of Sybaris (Italy)

The study of technology transfer in pottery production to the periphery of the Mycenaean world has been addressed by considering two different areas, southern Italy and central Macedonia. Technological features such as ceramic paste, decoration and firing have been determined for different ceramic groups established according to provenance criteria. The studies of technology and provenance have been performed following an archaeometric approach, using neutron activation analysis, petrographic analysis, X-ray diffraction and scanning electron microscopy. The results have revealed the existence of two different models. On the one hand, southern Italy seems to exhibit a more organized pottery production, which follows a Mycenaean-like technology, while in central Macedonia production is probably more varied, being based in part on the technology of the local tradition.

Electron scattering in isotonic chains as a probe of the proton shell structure of unstable nuclei

Electron scattering on unstable nuclei is planned in future facilities of the GSI and RIKEN upgrades. Motivated by this fact, we study theoretical predictions for elastic electron scattering in the N=82, N=50, and N=14 isotonic chains from very proton-deficient to very proton-rich isotones. We compute the scattering observables by performing Dirac partial-wave calculations. The charge density of the nucleus is obtained with a covariant nuclear mean-field model that accounts for the low-energy electromagnetic structure of the nucleon. For the discussion of the dependence of scattering observables at low-momentum transfer on the gross properties of the charge density, we fit Helm model distributions to the self-consistent mean-field densities. We find that the changes shown by the electric charge form factor along each isotonic chain are strongly correlated with the underlying proton shell structure of the isotones. We conclude that elastic electron scattering experiments on isotones can provide valuable information about the filling order and occupation of the single-particle levels of protons.