X-ray absorption near edge structures of DNA or its components around the oxygen K-shell edge

The initial process of radiation damage in DNA was investigated by measuring the X-ray absorption near edge structures (XANES) within the energy region around the oxygen K-shell absorption edge for DNA, cytosine and 2-deoxy-d-ribose. Irradiation and XANES experiments were performed with the BL23SU soft X-ray beamline, using synchrotron radiation from the 8 GeV electron storage ring at SPring-8. Samples were mounted on gold-coated plates in a vacuum chamber. The XANES spectra were obtained by measuring the photoelectron current of the samples. 2-Deoxy-d-ribose was exposed to X rays at the absorption peak corresponding to the oxygen (O) 1s-->sigma* transition energy (538 eV); the XANES spectra were obtained after each irradiation. DNA and cytosine, possessing characteristic XANES spectra, both had two major energy bands corresponding to the O 1s-->pi* and 1s-->sigma* transitions. Two new peaks appeared and gradually increased in the XANES spectra of 2-deoxy-d-ribose during irradiation. These results suggest that C-O bonds in 2-deoxy-d-ribose are transformed to C=O bonds by O 1s-->sigma* transition, suggesting that the molecules undergo chemical changes into carbonyl-containing compounds.     

Study of polynucleotide conformation by resolution-enhanced ultraviolet spectroscopy poly(rC) and poly(dC).

Self-deconvolution and the fourth derivative of ultraviolet absorption spectra have been used to study stacked single-stranded and double-helix structures of different cytosine-containing polynucleotides for the first time. These compounds were studied under different solution conditions (pH and organic solvents) and at low temperatures. The red shift of the lower band (B2u band plus possibly some n-->pi* transition) of the absorption spectra in the cytosine-containing polynucleotides and the appearance of new peaks in the deconvoluted and derivative spectra in the 280-310 nm region are attributed mainly to cytosine-cytosine stacking interactions. In particular, the fourth-derivative peaks at wavelengths higher than 290 nm can be associated to coupling of electronic transitions of cytosine bases. The nature of the electronic transitions producing the absorption bands which are resolved in the aforementioned fourth-derivative peaks is discussed. It is concluded that the resolution-enhancement techniques used in this work, i.e. self-deconvolution and fourth derivative, complement each other and are useful methods to study structural changes of single-stranded and double-stranded polynucleotides allowing, at the same time, more information to be obtained about specific stacking interactions than classical absorption spectrophotometry.     

Spectral dependence of energy transfer in wild-type peripheral light-harvesting complexes of photosynthetic bacteria

The precise position of the upper exciton component and relevant vibronic transitions of the B850 ring in peripheral light-harvesting complexes from purple photosynthetic bacteria are important values for determining the exciton bandwidth and electronic structure of the B850 ring. To determine the presence of these components in wild-type LH2 complexes the pump-probe femtosecond transient spectra obtained with excitation into the 730-840 nm spectral range are analyzed. We show that at excitation wavelengths less than 780 nm B850 absorption bands are present and that, in accordance with exciton theory, these bands peak further in the blue when the lowest optically allowed transition is more red-shifted.     

Interpretation of hypochromic and hyperchromic intensity changes in the Raman spectra of polypeptides and polynucleotides undergoing transition.

The hyperchromic and hypochromic changes in the intensity of the amide-I and amide-III lines of polypeptides and certain ring vibrations of the bases of polynucleotides are shown to be related to similar changes in the lower energy uv absorption bands. The selection rules strictly limit the pairs of excited electronic states that can contribute to the elements of the polarizability matrix. An energy-dependent term in this equation weights the contribution of the pairs of electronic transitions in favor of those involving the lower energy transitions. For both polypeptides and polynucleotides, there is a large hypochromic inensity change in the first π → π* exciton band upon the coil-to-helix transition. Through the selection rules, certain conformationally sensitive Raman lines are shown to derive their intensity predominantly from this band and hence also display hypochromism. Again, through an application of the selection rules, certain Raman lines can be demonstrated to depend predominantly for their intensity upon the n → π* transition, and consequently have the opposite hyperchromic intensity change upon the same conformational transition.     

Study of furanose ring flexibility in polynucleotide chains using Raman spectra analysis

The bands within the range of 800–850 cm^?1 of Raman spectra of polynucleotides sensitive to the change in conformation of sugar–phosphate backbone are analyzed theoretically. The bands are interpreted as the appearance of a quasi-local deoxyribose vibrational mode whose frequency is dependent on the ring puckering. The localization region of the vibrational mode is pointed out. The theory establishes a relationship between the observed spectral intensity and the population of deoxyribose conformational states described in the framework of the pseudorotation concept. The approach developed allowed one to describe the band shapes and their temperature behavior, and to determine the pseudorotation potential of deoxyribose in the helix B -form of A · T containing polynucleotides. Using the analysis of Raman spectra of DNA fibers in water–ethanol mixture the deoxyribose flexibility during the B -A transition is investigated in terms of the population of conformers and effective potential. It is shown that N- and S-type deoxyribose conformers are populated in the DNA B -form (those of the S-type are preferable), whereas N-type conformers are primarily populated in the DNA A -form.     

Synthesis and photophysical studies on a new fluorescent phenothiazine‐based derivative

A new typical phenothiazine compound functionalized with thienyl‐indandione derivative (PTZTID) was synthesized and characterized using spectral analysis (ultraviolet–visible (UV–vis) light, infrared (IR), ¹H nuclear magnetic resonance (NMR) and ¹³C NMR tools). The UV–vis absorption spectra of the PTZTID solution in 1,4‐dioxane showed two absorption bands attributed to localized aromatic π–π* transitions of conjugated aromatic moieties and intramolecular charge transfer with the characteristics of a π–π* transition. The fluorescence spectra exhibited a maximum emission wavelength at 580 nm. The effect of concentration on photophysical properties took the form of a minor hypsochromic shift, which was attributed to some extent to the occurrence of H‐type aggregation of the PTZTID derivative. Binary solvent effects on the spectroscopic behaviour of PTZTID were measured at different H₂O/1,4‐dioxane ratios. Similarly, when increasing the water content, a hypsochromic shift was observed that resulted from H‐type aggregation. Furthermore, geometry and electronic configurations of PTZTID were studied at density functional theory /B3LYP level and indicated that the compound had a nonplanar (butterfly structure).     

Preparation and characterization of cobalt(II), nickel(II) and copper(II) complexes with water-soluble macrocyclic N4-ligands: 6,15-diethyl-4,13-dihydro-1,10-dimethyl-(E)-dipyridinio [b,i] [1,4,8,11] tetraazacyclotetradecine iodide or methyl sulfate

The mixture of 6,15-diethyl-4,13-dihydro-(E)-dipyrido [b,i] [1,4,8,11] tetraazacyclotetradecine (2-E) and 6,15-diethyl-4,13-dihydro-(Z)-dipyrido [b,i][1,4,8,11] tetraazacyclotetradecine (2-Z) was prepared by cyclization of 3,4-diaminopyridine and 2-ethyl-3-ethoxyacrolein. Two kinds of isomers were separated by repeated recrystallization from chloroform. Methylation of pyridine comprised in 2-E using iodomethane or dimethyl sulfate afforded the corresponding dimethylated product (2-E-I or 2-E-S), which is soluble in water. The cobalt(II), nickel(II) and copper(II) complexes of 2-E-I and 2-E-S were prepared. The absorption bands appearing in the energy range greater than 18 000 cm⁻¹ were attributed to the π → π* transitions within a ligand molecule and CT transitions from metal to ligand. Since the d → d* bands for nickel(II) and copper(II) complexes were obscured by the π → π* and CT bands, no significant absorption bands were found in the region more than 18000 cm⁻¹. One of the d → d* bands for the cobalt(II) complex was observed at around 13 000 cm⁻¹. These complexes assume the square- planar structures. A strong IR band due to the CN stretching mode of the macrocycle moiety was observed at ca. 1640 cm−1 and shifted slightly toward lower energy upon metal-coordination, cis (2-Z) and trans (2-E) isomers in the present macrocycle can be judged by the amine proton signals of NMR spectra. All proton signals except for amine protons show downfield shifts due to the deshielding effect of the positive charge provided by methylation of pyridine contained in the metal-free macrocycle. Upon formation of the nickel(II) complex all proton signals, except the aromatic protons adjacent to the nitrogen atom of a pyridine ring, also show a downfield shift, which is attributed to the deshielding effect based on the positive charge given by nickel(II). The intensity change of the electronic spectrum at 425 nm is available for the determination of copper(II) concentrations in the aqueous solution using the water-soluble macrocycles (2-E-I and 2-E-S) and a good linear correlation is observed up to 8 × 10⁻⁶ mol dm⁻³.     

Interruption of the MnO2 oxidative process on dopamine and L-dopa by the action of S2O3(2-)

The oxidation effects of Mn2+, Mn3+ or MnO2 on dopamine can be studied in vitro and, therefore, this offers a model of the auto-oxidation process that appears naturally in neurons causing Parkinson's disease. The use of MnO, as an oxidizer in aqueous solution at pH 7 causes the oxidation of catecholamines (L-dopa, dopamine, noradrenaline and adrenaline) to melanin. However, this work shows that, in water at pH 6-7, the oxidation of catecholamines by MnO2 in the presence of sodium thiosulphate (Na2S2O3) occurs by other mechanisms. For dopamine and L-dopa, MLCT complexes were formed with bands at 312, 350 (sh), 554 (sh) nm, and an intense band at 597 nm (epsilon approximately/= 4 x 10(3) M(-1) cm(-1)) and at ca. 336, 557 (sh) nm, and an intense band at 597 nm (epsilon approximately 6 x 10(3) M(-1) cm(-1)), respectively. The latter transitions were assigned to d(pi)-->pi*-SQ. Noradrenaline and adrenaline do not form this blue complex in solution, but generate soluble oxidized compounds. The resonance Raman spectra of these complexes in solution showed bands at 950, 1006, 1258, 1378, 1508 and 1603 cm(-1) for the complex derivation of L-dopa and at 948, 1010, 1255, 1373, 1510 and 1603 cm(-1) for the dopamine-derived compound. The most intense Raman band at ca. 1378 cm(-1) was assigned to C-O stretching with major C1-C2 characteristics and indicated that dopamine and L-dopa do not occur complexed with manganese in the catecholate or quinone form, but suggests an intermediate compound such as an anionic o-semiquinone (SQ-), forming a complex such as [Mn(II)(SQ-)3]-. All enhanced Raman frequencies are characteristic of the benzenic ring without the participation of the aminic nitrogen. A mechanism is proposed for the formation of the dopamine and L-dopa complexes and a computational simulation was performed to support it.     

IR study of base stacking interactions.

For D2O solutions of 1,3-dimethyluracil, cytidine, caffeine, inosine and 2'-deoxyadenosine the concentration dependence of IR spectra (1800-1400 cm-1) have been found which reflects stacking association of these compounds. A method is proposed to use this data to obtain thermodynamic parameters of association and the molecular spectra in the monomer and associated forms. The homoassociation constant for 1,3-dimethyluracil was estimated as k=0.65. Stacking is shown to change radically the spectra, inducing a high-frequency shift of carbonyl vibrations and a decrease in the intensity of skeletal stretching vibration bands. This allows one to distinguish between the stacking interactions and hydrogen bonding. A conclusion is made about the considerable contribution of stacking interactions into the change of IR spectra of DNA and other polynucleotides following conformational transitions.     

Raman spectroscopic study of 2H- and 15N- substituted guanosines: Monomers,gels, and polymers

¹⁵N-labeled guanosines were synthesized and studied by Raman spectroscopy. The isotopic substitution was either on nitrogens 1, 2, and 3 or on nitrogens 7 and 9. These substituted guanosines and their partially or totally deuterated derivatives were compared under a variety of experimental conditions: in aqueous solution in the presence of 0.1M KCl at pH 7 at 60 and 10°C, i.e., in solution and in gel form. The sensitivity to nitrogen isotopic substitution of some of the “hypochromic” bands was defined. These spectra were also compared with those in acidic and basic solution. The body of these data was compared with the results on poly(guanylic acid) and on guanine-containing polynucleotides and nucleic acids.     

Electronic structures of azulene-fused porphyrins as seen by magnetic circular dichroism and TD-DFT calculations

A combination of magnetic circular dichroism (MCD), electronic absorption spectroscopy and time-dependent density functional theory (TD-DFT) calculations has been used to investigate the electronic structure of azulene-fused pi-expanded porphyrins based primarily on the spectral properties of absorption bands in the near infrared region. From MCD experiments, it was suggested that in the case of a mono-azulene-fused porphyrin DeltaHOMO approximately equal DeltaLUMO (where DeltaHOMO is the magnitude of the energy gap between the HOMO and HOMO-1 and DeltaLUMO is the magnitude of the energy gap between the LUMO and LUMO+1), while in the case of an oppositely-di-azulene-fused porphyrin, DeltaHOMO相似文献   

FTIR detection of water reactions in the oxygen-evolving centre of photosystem II

Flash-induced Fourier transform infrared (FTIR) difference spectroscopy has been used to study the water-oxidizing reactions in the oxygen-evolving centre of photosystem II. Reactions of water molecules were directly monitored by detecting the OH stretching bands of weakly H-bonded OH of water in the 3700-3500 cm(-1) region in FTIR difference spectra during S-state cycling. In the S1-->S2 transition, a band shift from 3588 to 3617 cm(-1) was observed, indicative of a weakened H-bond. Decoupling experiments using D2O:H2O (1:1) showed that this OH arose from a water molecule with an asymmetric H-bonding structure and this asymmetry became more significant upon S2 formation. In the S2-->S3, S3-->S0 and S0-->S1 transitions, negative bands were observed at 3634, 3621 and 3612 cm(-1), respectively, representing formation of a strong H-bond or a proton release reaction. In addition, using complex spectral features in the carboxylate stretching region (1600-1300 cm-(1)) as 'fingerprints' of individual S-state transitions, pH dependency of the transition efficiencies and the effect of dehydration were examined to obtain the information of proton release and water insertion steps in the S-state cycle. Low-pH inhibition of the S2-->S3, S3-->S0 and S0-->S1 transitions was consistent with a view that protons are released in the three transitions other than S1-->S2, while relatively high susceptibility to dehydration in the S2-->S3 and S3-->S0 transitions suggested the insertion of substrate water into the system during these transitions. Thus, a possible mechanism of water oxidation to explain the FTIR data is proposed.     

Mn K-edge XANES spectroscopy of a photosynthetic O2-evolving complex. High-quality pre-edge features and distinct fine structures in the S1- and S2-states

High-resolution XANES (X-ray Absorption Near Edge Structure) spectroscopy for Mn in the S1 and S2 states of the spinach photosynthetic O2-evolving complex revealed distinct features in K-edge spectra, when a high signal-to-noise (S/N) ratio of ca. 80 with a low and constant background-to-signal (B/S) ratio of 0.15 to 0.18 was attained. Six features resolved in each S-state spectrum involve a pre-edge feature due to 1s----3d transitions, a main-edge feature possibly due to 1s----4s transitions and four fine structures superimposed on the principal absorption bands due to 1s----4p* transitions. The high-quality pre-edge features were analyzed according to a parametric ligand-field theory in comparison with those of some typical authentic Mn complexes. It was deduced that i) all of the four Mn ions in the S1-state are octahedrally coordinated and two of them constitute a di-mu-oxo bridged Mn(III, III) dimeric subunit; ii) the bridged Mn(III) ions are further bridged by a deprotonated water dimer, (HOHOH)-, and coordinated by imidazole-N and carboxylate-O- on the opposite side of the Mn atom from the di-mu-oxo bridge; iii) the other two Mn ions exist in the form of Mn(III) monomeric subunits; and iv) upon the S1----S2 transition, only the bridged Mn(III,III) is oxidized to Mn(III,IV). The distinct change in the principal absorption band shape upon the S1----S2 transition is briefly discussed to obtain the XANES evidence for a tetrameric Mn-cluster.     

Resonance Raman enhancement of FeIV=O stretch in high-valent iron porphyrins: an insight from TD-DFT calculations

Density functional theory (DFT) has been applied to explain the origin of resonance Raman enhancement associated with the Fe(IV)=O stretch observed in iron(IV)oxo porphyrins. To accomplish this electronic excitations of the Im-(Por)Fe(IV)=O model were computed in the 1.5-4.0 eV spectral range using time-dependent DFT (TD-DFT). All electronic transitions having dominant pi-->pi* character were analyzed and assigned in terms of one-electron excitations. It was found that the most intense Soret band has a multi-component character, but the pi (a(2u))-->pi*(d(xz),d(yz)) and pi (a(1u))-->pi*(d(xz),d(yz)) electronic excitations are primarily responsible for observed resonance enhancement of the Fe(IV)=O stretch.     

Electron-oscillatory spectra of pyrimidine bases of nucleic acids in argon matrices

The studies on the oscillatory structure of adsorption spectra of pyrimidine bases of nucleic acids isolated in Ar matrix at 11 K are described. To clear up the importance of molecule isolation in the matrix, amorphous films of the materials studied were investigated experimentally at 11 and 77 K. The work was carried out using the low temperature optic attachment developed by the authors. The long wavelength band of cytosine and deuterocytosine in the matrix is shown to consist of two bands: 1) lambda max = 267 nm with oscillatory progressions of 500 and 400 cm-1, respectively, and 2) lambda max = 280 nm with progression approximately 800 cm-1. The first pi pi*-absorption band of 1-methylcytosine has a single oscillatory progression 470 cm-1. Thymine and uracil in Ar matrices form diffuse structural spectra of 630 and 660 cm-1, respectively. The oscillatory progressions are attributed to the oscillatory frequencies of the pyrimidine molecule ring oscillations in the excited state. The annealing of the matrix results for all the materials in smearing the oscillatory molecule structure up to its complete vanishing. In film samples the oscillatory structure is not seen at low temperatures.     

Theoretical CD studies of polypeptide helices: examination of important electronic and geometric factors

An improved model for calculating the CD of polypeptides has been developed. Excited state wavefunctions were derived from CNDO/S (complete neglect of differential overlap, spectroscopic) calculations on N-methylacetamide. Four discrete peptide-localized transitions were employed: pi 0 pi* (NV1), pi* + pi* (NV2), n pi*, and n' pi*. Inclusion of the pi + pi transition (lambda 0 = 140 nm) significantly improves the accuracy of the calculated CD spectra in the 180-250-nm region. Spectra were computed for various helical structures, including right-handed alpha-, alpha II-, omega-, pi-, 3(10-), and poly (proline) I-helices, and the left-handed poly (proline) II-helix. Sensitivity to changes in the peptide backbone geometry and chain length are examined. Electronic factors such as ground-state charge distribution, hybridization effects, and basis set deorthogonalization have been investigated. The nonconservative nature of the poly (Pro) I and II CD spectra is reproduced, and the helix band present in earlier exciton calculations on the alpha-helix has been diminished.     

Polarised absorption spectroscopy of chlorophyll-lipid membranes

A technique has been developed for measuring visible absorption spectra of chlorophyll in lipid membranes. An expression is derived which enables the directions of the transition moments of the different absorption bands to be determined from polarisation data. It is found that the transition moments of the principal blue and red absorption bands of chlorophyll a make angles of 26° and 36.5° respectively with the plane of the membrane. On the assumption that these two transitions lie in the plane of the porphyrin ring and are mutually perpendicular, it may be deduced that the plane of the porphyrin ring is tilted at approx. 48° to the membrane surface. For chlorophyll b the transition moments of the blue and red bands are found to make angles of 29.5° and 36.5° with the plane of the bilayer, giving an angle of tilt of the porphyrin ring of approx. 51°.

These results are compared with measurements of dichroism in vivo.     

In vivo prediction of the nutrient status of individual microalgal cells using Raman microspectroscopy

An in vivo method for predicting the nutrient status of individual algal cells using Raman microspectroscopy is described. Raman spectra of cells using 780 nm laser excitation show enhanced bands mainly attributable to chlorophyll a and beta-carotene. The relative intensities of chlorophyll a and beta-carotene bands changed under nitrogen limitation, with chlorophyll a bands becoming less intense and beta-carotene bands more prominent. Although spectra from N-replete and N-starved cell populations varied, each distribution was distinct enough such that multivariate classification methods, such as partial least squares discriminant analysis, could accurately predict the nutrient status of the cells from the Raman spectral data.