X-ray absorption spectroscopy of the nucleotide bases at the carbon, nitrogen, and oxygen K-edges

Near-edge X-ray absorption fine structure spectra of three pyrimidine (viz., cytosine, uracil, and thymine) and two purine (viz., adenine and guanine) nucleobases, which are the key constituents of DNA and RNA, were measured at the C, N, and O K-edges using the self-absorption-free partial electron yield mode. The nucleobase samples were prepared as highly pure native polycrystalline powder films. The spectra are analyzed in terms of the electronic structure of the nucleobases. Subtle chemical effects related to the molecular structures of these heterocyclic compounds with extended pi-electron systems are considered and discussed.     

Interpretation of EPR and optical spectra of Ni(II) ions in crystalline lattices at ambient temperature

Many biologically important paramagnetic metal ions are characterized by electron paramagnetic resonance (EPR) spectroscopy to use as spin probes to investigate the structure and function of biomolecules. Though nickel(II) ions are an essential trace element and part of many biomolecules, the EPR properties are least understood. Herein, the EPR and optical absorption spectra measured at 300 K for Ni(II) ions diluted in two different diamagnetic hosts are investigated and reported. The EPR spectrum of a polycrystalline Ni/Mg(3-methylpyrazole)₆(ClO₄)₂ [Ni/MMPC] shows two transitions at X-band frequency (~9.5 GHz), suggesting the zero-field splitting parameter (D) is larger than the resonance field of the free electron (H_o). This incomplete and complex spectrum is successfully analyzed to obtain EPR parameters. The EPR spectrum of the polycrystalline Ni/Zn(pyrazole)₆(NO₃)₂ [Ni/ZPN] shows a triplet spectrum indicating D < H_o. A detailed analysis of single-crystal EPR data yielded the spin Hamiltonian parameters. The optical absorption spectra are deconvoluted to understand the symmetry of the coordination environment in the complex.     

EPR and IR spectral investigations on some leafy vegetables of Indian origin

EPR spectral investigations have been carried out on four edible leafy vegetables of India, which are used as dietary component in day to day life. In Rumex vesicarius leaf sample, EPR spectral investigations at different temperatures indicate the presence of anti-ferromagnetically coupled Mn(IV)–Mn(IV) complexes. EPR spectra of Trigonella foenum graecum show the presence of Mn ions in multivalent state and Fe³⁺ ions in rhombic symmetry. EPR spectra of Basella rubra indicate the presence of Mn(IV)–O–Mn(IV) type complexes. The EPR spectra of Basella rubra have been studied at different temperatures. It is found that the spin population for the resonance signal at g = 2.06 obeys the Boltzmann distribution law. The EPR spectra of Moringa oliefera leaves show the presence of Mn²⁺ ions. Radiation induced changes in free radical of this sample have also been studied. The FT-IR spectra of Basella rubra and Moringa oliefera leaves show the evidences for the protein matrix bands and those corresponding to carboxylic CO bonds.     

Studies on Intramolecular Charge Transfer Fluorescence Probe and DNA Binding Characteristics

An intramolecular charge transfer fluorescence probe of 4′-N,N-dimethylamino-4-amino-chalcone(DMAC) exhibits characteristics clearly correlated with the polarity of solvents. The interaction of this fluorescence probe with calf thymus DNA has been investigated. Generally, DMAC bound to DNA shows marked changes in fluorescence and absorbance properties compared to the spectral characteristics of the free form in solution phase. In the presence of DNA the fluorescence intensity of DMAC is greatly increased with a large bathochromic shift of excitation and emission wavelengths. A hypochromism in absorption spectrum was also observed. The absorption and fluorescence spectra, salt concentration effect, and KI quenching experiments demonstrate that DMAC molecule as an intercalator is inserted into the base-stacking domain of DNA double helix, and the interaction of the nucleobases with DMAC molecule causes the increase of fluorescence intensity and hypochromism in absorption spectrum. The intrinsic binding constant and the binding site number were estimated to be 7.04 × 10⁶ mol L⁻¹ in base pairs and 0.065, respectively. The I/I₀ vs DNA concentration plot shows a linear range covering 1.98 × 10⁻⁶ to 2.08 × 10⁻⁴ mol L⁻¹ in base pairs which can be used for determining DNA with a detection limit of 6.0 × 10⁻⁷ mol L⁻¹ in base pairs (0.6 μg ml⁻¹).     

Iron-modified mesoporous SBA-15 silica: Preparation and characterization studies

Fe-SBA-15 materials with different Si/Fe ratios (Si/Fe = 100, 60, 15) have been synthesized by hydrothermal method and characterized by several spectroscopic techniques. Electron spin resonance and Mössbauer spectroscopy, along with electron microscopy and X-ray diffraction, allowed differentiation of several iron species. These species correspond to hematite particles, very small “isolated” or oligomeric Fe^III species possibly incorporated in the mesoporous silica wall, and Fe^III oxide clusters either isolated or agglomerated, forming “rafts” at the surface of the silica and exhibiting ferromagnetic ordering. Because of their agglomeration, these clusters appear with a two-peak size distribution, with one peak corresponding to the isolated clusters formed in the mesopores and still embedded in them and the other corresponding to the agglomerates spread on the surface of the mesoporous silica particles.     

Preparation and study of copper(II) proprionate complex with papaverine

The synthesis and characterization of Cu(CH₃CH₂COO)₂·papaverine is reported. The characterization of the compound was based on elemental and thermal analysis, on electronic and EPR spectra, as well as magnetic measurements over the temperature range. The available evidence supports a binuclear structure. The EPR spectrum is consistent with spin S = 1. The exchange interaction parameter −2J = 362 cm⁻¹. Correlation between the −2J values in familiar copper(II) proprionates and pKa values of the axial ligands was found and discussed.     

Uptake of Cell-Penetrating Peptide RL2 by Human Lung Cancer Cells: Monitoring by Electron Paramagnetic Resonance and Confocal Laser Scanning Microscopy

RL2 is a recombinant analogue of a human κ-casein fragment, capable of penetrating cells and inducing apoptosis of cancer cells with no toxicity to normal cells. The exact mechanism of RL2 penetration into cells remains unknown. In this study, we investigated the mechanism of RL2 penetration into human lung cancer A549 cells by a combination of electron paramagnetic resonance (EPR) spectroscopy and confocal laser scanning microscopy. EPR spectra of A549 cells incubated with RL2 (sRL2) spin-labeled by a highly stable 3-carboxy-2,2,5,5-tetraethylpyrrolidine-1-oxyl radical were found to contain three components, with their contributions changing with time. The combined EPR and confocal-microscopy data allowed us to assign these three forms of sRL2 to the spin-labeled protein sticking to the membrane of the cell and endosomes, to the spin-labeled protein in the cell interior, and to spin labeled short peptides formed in the cell because of protein digestion. EPR spectroscopy enabled us to follow the kinetics of transformations between different forms of the spin-labeled protein at a minimal spin concentration (3–16 μM) in the cell. The prospects of applications of spin-labeled cell-penetrating peptides to EPR imaging, DNP, and magnetic resonance imaging are discussed, as is possible research on an intrinsically disordered protein in the cell by pulsed dipolar EPR spectroscopy.     

Electron spin relaxation time of Ni(II) ion in hexapyrazole zinc(II) dinitrate at 300 K

Understanding the electron spin relaxation properties of paramagnetic species is a fundamental requirement to use them as a probe to measure distances between sites in biomolecules by electron paramagnetic resonance (EPR) spectroscopy. Even though Ni(II) ion is an essential trace element for many species, relaxation properties are not well understood. Herein, the polycrystalline sample of Ni(II) ion magnetically diluted in Zn(Pyrazole)₆(NO₃)₂ (Ni/ZPN) has been studied in detail by EPR spectroscopy to explore the electron spin relaxation time. Progressive continuous-wave (CW) EPR power saturation study on Ni/ZPN at 300 K yielded 907 mW as the P_1/2 value. The cavity constant (K_Q) has been calculated using tempol in PVA-BA glass matrix and the product of electron spin-lattice relaxation time (T₁) and spin–spin relaxation time (T₂) for Ni/ZPN at 300 K has been reported for the first time.     

Single crystal EPR and optical studies of paramagnetic ions doped zinc potassium phosphate hexahydrate—Part II: VO(II)—a case of substitutional site

Single crystal electron paramagnetic resonance (EPR) studies were carried at room temperature for VO(II) doped zinc potassium phosphate hexahydrate. The results indicate that the paramagnetic impurity has entered the lattice only substitutionally, as confirmed by the single crystal rotations. The spin Hamiltonian parameters calculated from the spectra are g_//=1.9356, g=1.9764, A_//=200.9 G and A=76.5 G. The optical absorption spectrum exhibits three bands (800, 670 and 340 nm) suggesting the C_4v symmetry and the optical parameters evaluated are Dq=1492, Ds=−3854 and Dt=186 cm⁻¹.     

Electron self-exchange kinetics determined by MARY spectroscopy: theory and experiment

The electron self-exchange between a neutral molecule and its charged radical, which is part of a spin-correlated radical ion pair, gives rise to line width effects in the fluorescence-detected MARY (magnetic field effect on reaction yield) spectrum similar to those observed in EPR spectroscopy. An increasing self-exchange rate (i.e., a higher concentration of the neutral molecule) leads to broadening and subsequent narrowing of the spectrum. Along with a series of MARY spectra recorded for several systems (the fluorophores pyrene, pyrene-d(10) and N-methylcarbazole in combination with 1,2- and 1,4-dicyanobenzene) in various solvents, a theoretical model is developed that describes the spin evolution and the diffusive recombination of the radical pair under the influence of the external magnetic field and electron self-exchange, thereby allowing the simulation of MARY spectra of the systems investigated experimentally. The spin evolution of the radicals in the pair is calculated separately using spin correlation tensors, thereby allowing rigorous quantum mechanical calculations for real spin systems. It is shown that the combination of these simulations with high resolution, low noise experimental spectra makes the MARY technique a novel, quantitative method for the determination of self-exchange rate constants. In comparison to a simple analytical formula which estimates the self-exchange rate constant from the slope of the linear part of a line width vs concentration plot, the simulation method yields more reliable and accurate results. The correctness of the results obtained by the MARY method is proved by a comparison with corresponding data from the well-established EPR line broadening technique. With its less stringent restrictions on radical lifetime and stability, the MARY technique provides an alternative to the classical EPR method, in particular for systems involving short-lived and unstable radicals.     

A long-lived charge-separated state of spiro compact electron donor–acceptor dyads based on rhodamine and naphthalenediimide chromophores

Spiro rhodamine (Rho)-naphthalenediimide (NDI) electron donor–acceptor orthogonal dyads were prepared to generate a long-lived charge separation (CS) state based on the electron spin control approach, i.e. to form the ³CS state, not the ¹CS state, to prolong the CS state lifetime by the electron spin forbidden feature of the charge recombination process of ³CS → S₀. The electron donor Rho (lactam form) is attached via three σ bonds, including two C–C and one N–N bonds (Rho-NDI), or an intervening phenylene, to the electron acceptor NDI (Rho-Ph-NDI and Rho-PhMe-NDI). Transient absorption (TA) spectra show that fast intersystem crossing (ISC) (<120 fs) occurred to generate an upper triplet state localized on the NDI moiety (³NDI*), and then to form the CS state. For Rho-NDI in both non-polar and polar solvents, a long-lived ³CS state (lifetime τ = 0.13 μs) and charge separation quantum yield (Φ_CS) up to 25% were observed, whereas for Rho-Ph-NDI (τ_T = 1.1 μs) and Rho-PhMe-NDI (τ_T = 2.0 μs), a low-lying ³NDI* state was formed by charge recombination (CR) in n-hexane (HEX). In toluene (TOL), however, CS states were observed for Rho-Ph-NDI (0.37 μs) and Rho-PhMe-NDI (0.63 μs). With electron paramagnetic resonance (EPR) spectra, weak electronic coupling between the Rho and NDI moieties for Rho-NDI was proved. Time-resolved EPR (TREPR) spectra detected two transient species including NDI-localized triplets (formed via SOC-ISC) and a ³CS state. The CS state of Rho-NDI features the largest dipolar interaction (|D| = 184 MHz) compared to Rho-Ph-NDI (|D| = 39 MHz) and Rho-PhMe-NDI (|D| = 41 MHz) due to the smallest distance between Rho and NDI moieties. For Rho-NDI, the time-dependent e,a → a,e phase change of the CS state TREPR spectrum indicates that the long-lived CS state is based on the electron spin control effect.

Spiro compact rhodamine-naphthalenediimide electron donor–acceptor dyads show a long-lived charge separated state (lifetime: 0.72 μs) based on the electron spin control effect were reported.     

Voltage-Height Spectroscopy in the <Emphasis Type="Italic">Ex Situ</Emphasis> Configuration of a Scanning Tunneling Microscope

Basic regularities of electrochemical processes in the gap of an ex situ scanning tunneling microscope in conditions of condensation of air moisture at the sample surface are considered on a qualitative level. A layer of condensed moisture is viewed as an electrolyte in a two-electrode cell. The depolarizers present in this layer may experience electrochemical conversions on the tip and in an area of the sample surface near the tip. As a result, the recorded “tunneling” current includes electrochemical constituents. Depending on the electrochemical processes in the gap, various dependences of the tip-sample distance on the current and applied voltage can be expected. For preliminary diagnostics of processes in the gap it is suggested to use voltage-height spectra, whose shape and characteristic heights are sensitive to the nature and location of redox active species. Experimental data for various films on conducting supports (quasi-two-dimensional adsorbed layers of hemin and peroxidase, electrodeposited nonstoichiometric tungsten oxides, doped tin dioxide, solid electrolyte with ionic conduction) are presented as an examples.__________Translated from Elektrokhimiya, Vol. 41, No. 5, 2005, pp. 583–595.Original Russian Text Copyright © 2005 by Yusipovich, Vassiliev.     

Spectral change in X-ray absorption near edge structure of DNA thin films irradiated with monochromatic soft X-rays

To reveal the chemical changes induced in DNA by irradiation with ionizing radiation, we have investigated the spectral change in the X-ray absorption near edge structure (XANES) of DNA resulting from exposure to monochromatic soft X-rays. We used a thin film of calf thymus DNA as a sample and observed nitrogen K-shell and oxygen K-shell XANES spectra. The typical monochromatic soft X-ray energies used for the irradiation (395, 408, 528, and 538 eV) were obtained from a soft X-ray beamline (BL23SU, SPring-8). These energies correspond to those just below or just above the nitrogen and oxygen K-shell ionization energy, respectively. The obtained XANES spectra show significant changes by irradiation. Particularly a new π* resonance peak in oxygen XANES spectra evidently appeared by the irradiation above oxygen K-shell ionization potential. These results suggest that carbonyl groups, presumably a propenal group (OC–CC), may be produced in the sample by oxygen ionization. Thus characteristic damage induced by induction in the DNA molecule would be predicted following exposure to monochromatized synchrotron soft X-rays.     

EPR and optical absorption studies of Cr ions in d-gluconic acid monohydrate

EPR studies are carried out on Cr³⁺ ions doped in d-gluconic acid monohydrate (C₆H₁₂O₇·H₂O) single crystals at 77 K. From the observed EPR spectra, the spin Hamiltonian parameters g, |D| and |E| are measured to be 1.9919, 349 (×10⁻⁴) cm⁻¹ and 113 (×10⁻⁴) cm⁻¹, respectively. The optical absorption of the crystal is also studied at room temperature. From the observed band positions, the cubic crystal field splitting parameter Dq (2052 cm⁻¹) and the Racah interelectronic repulsion parameter B (653 cm⁻¹) are evaluated. From the correlation of EPR and optical data the nature of bonding of Cr³⁺ ion with its ligands is discussed.     

Original close-packed structure and magnetic properties of the Pb4Mn9O20 manganite

The crystal structure of the Pb₄Mn₉O₂₀ compound (previously known as “Pb_0.43MnO_2.18”) was solved from powder X-ray diffraction, electron diffraction, and high resolution electron microscopy data (S.G. Pnma, a=13.8888(2) Å, b=11.2665(2) Å, c=9.9867(1) Å, R_I=0.016, R_P=0.047). The structure is based on a 6H (cch)₂ close packing of pure oxygen “h”-type (O₁₆) layers alternating with mixed “c”-type (Pb₄O₁₂) layers. The Mn atoms occupy octahedral interstices formed by the oxygen atoms of the close-packed layers. The MnO₆ octahedra share edges within the layers, whereas the octahedra in neighboring layers are linked through corner sharing. The relationship with the closely related Pb₃Mn₇O₁₅ structure is discussed. Magnetization measurements reveal a peculiar magnetic behavior with a phase transition at 52 K, a small net magnetization below the transition temperature, and a tendency towards spin freezing.     

Catalytic chemistry of transition metal ions on oxide surfaces. A molecular approach using EPR techniques

The applications of EPR spectroscopy to the study of catalysis and surface chemistry of oxides are reviewed. The specific features of the EPR spectra of catalytic materials are described and the means employed to enhance the amount of information that can be extracted from the spectra are discussed. Selected recent examples illustrate the possibilities offered by EPR techniques to the understanding of catalyst preparation, of the nature of active sites and reaction intermediates as well as of catalytic reaction mechanisms. One of the advantages of EPR is the possibility to investigate electron transfer phenomena (metal to ligand, ligand to metal or ligand to ligand) occurring between the surface transition metal ions and the adsorbed molecules. © 2000 Académie des sciences / Éditions scientifiques et médicales Elsevier SASEPR / catalysis / oxides / adsorption / reaction mechanisms / surface / electron transfer     

Superactive and stereospecific catalysts. III. Definitive identification of active sites by electron paramagnetic resonance

Superactive Ziegler–Natta catalysts have been prepared from a soluble MgCl₂·2-ethyl hexanol adduct in the presence of organic esters through reactions with TiCl₄ and activated with AlEt₃/phenyltriethoxy-silane. Electron paramagnetic spectra (EPR) were used to elucidate the nature and amount of those Ti⁺³ ions not bridged to another Ti⁺³ ion; the chlorine bridged Ti⁺³ ions are EPR silent. The EPR spectra were attributed to two rhombic Ti⁺³ sites with principal values for the g-tensors (1.967, 1.949, 1.915; and 1.979, 1.935, 1.887). The total amount of the EPR species, obtained by double integration of the EPR spectra, is in close agreement with the concentration of isospecific catalytic sites determined by radiotagging. This suggests that the nonspecific sites are EPR silent. When o-phthalic ester was present during the catalyst synthesis, there appears an EPR signal at the free electron g-value. This signal was attributed to a Ti⁺³ phthalate species with resonance stabilization and spin delocalization; it is absent in the catalysts made in the presence of monoesters such as ethyl benzoate. The effects of monomer, O₂, H₂O, and I₂ on the EPR spectra were investigated. The changes in the EPR spectral intensity and the total Ti⁺³ ions, the latter determined by redox titrations during a polymerization or catalyst aging, are described. The results were extensively compared with those observed for supported Ziegler–Natta catalyst prepared with crystalline MgCl₂.     

Effects of anionic surfactant SDS on the photophysical properties of two fluorescent molecular sensors

Two fluorescent molecular sensors CS1 and CS2 were designed and synthesized to probe the aggregate behavior of anionic surfactant SDS. CS1 was based on the photo-induced electron transfer (PET) mechanism, while CS2 was founded on the intramolecular charge transfer (ICT) mechanism. The photophysical properties of CS1–2 in anionic surfactant sodium dodecyl sulfate (SDS) solution were studied by fluorescence and UV–vis methods. The experimental results show that significant absorption and emission spectral responses of CS1 were observed with the addition of SDS: the absorbance and fluorescence intensity decreased first and then increased. The plot of fluorescence intensity of CS1 versus SDS concentration showed two break points, which might be ascribed to the critical micellar concentration (cmc) and the formation of premicelle (cac) aggregate, respectively. But the solution’s color of CS2 changed from yellow to red with increasing SDS concentrations. The large red-shift in both absorption (50 nm) and emission (55 nm) spectra of CS2 was resulted from the protonation of the electron accepting moiety (NC nitrogen), which enhanced the “push–pull” interaction of the ICT fluorophore. This was facilitated by the increase of local H⁺ concentration around SDS premicelle and micelle. As a consequence, pK_a values of CS1 and CS2 were elevated in SDS micelle.     

Magnetic and EPR Studies of α-, β-, and γ-Fe2WO6 Phases at Low Temperatures

The polymorphic modifications α-, β-, and γ-Fe₂WO₆ of the iron tungstate system were studied by means of magnetic susceptibility and EPR measurements at low temperatures. Both methods revealed a significant paramagnetic contribution, probably resulting from local distortions of the antiferromagnetic bulk structure induced by a disturbed cation ordering or the presence of Fe²⁺ ions. The magnetic susceptibility revealed a peak at 260 K for all samples which can be related with an AF phase transition. The EPR spectra comprised the contribution of various isolated paramagnetic iron centers, one arising from high-spin Fe³⁺ ions in rhombic crystal field symmetry with E/D ≈ 1/3 and D ≈ 0.22 cm^-1, an anisotropic EPR signal consistent with an S= 3/2 ground state with large zero-field splitting, and a dominant component in the g ≈ 2 region presumably arising from an S = 1/2; spin state. The latter spectra were tentatively attributed to the formation of multi-iron clusters, one of them invoking the presence of Fe²⁺ ions as well. For the βFe₂WO₆ phase an additional EPR spectrum was observed, which probably results from high-spin Fe³⁺ ions in a weak crystal field.     

Desorption electrospray ionization mass spectrometry of DNA nucleobases: implications for a liquid film model

Desorption electrospray ionization (DESI) mass spectrometry has been implemented on a commercial ion‐trap mass spectrometer and used to optimize mass spectrometric conditions for DNA nucleobases: adenine, cytosine, thymine, and guanine. Experimental parameters including spray voltage, distance between mass spectrometer inlet and the sampled spot, and nebulizing gas inlet pressure were optimized. Cluster ions including some magic number clusters of nucleobases were observed for the first time using DESI mass spectrometry. The formation of the cluster species was found to vary with the nucleobases, acidification of the spray solvent, and the deposited sample amount. All the experimental results can be explained well using a liquid film model based on the two‐step droplet pick‐up mechanism. It is further suggested that solubility of the analytes in the spray solvent is an important factor to consider for their studies by using DESI. Copyright © 2009 John Wiley & Sons, Ltd.