Electronic structure of the nucleobases

We present a comparison between experimental and calculated soft X-ray spectra of DNA's nucleobases, adenine (A), guanine (G), cytosine (C), and thymine (T) using X-ray absorption spectroscopy (XAS) and soft X-ray emission spectroscopy (XES). Spectra of the 1s thresholds of carbon, nitrogen, and oxygen give a complete picture of the occupied and unoccupied partial density of states of the nucleobases. A combination of both Hartree-Fock and density functional theory calculations are used in the comparison to experimental results. Most experimental results agree well with our theoretical calculations for the XAS and XES of all bases. All spectral features are assigned. A comparison of the experimental highest occupied molecular orbital-lowest unoccupied molecular orbital energy gaps is made to the diverse values predicted in the literature.     

Electronic structure and biological activity of nucleobases

HeI and HeII photoelectron spectra of 6-chloro-1,3-dimethyluracil have been measured. The assignment of the spectrum was made by comparison with photoelectron spectra of related compounds and by high-level OVGF calculations. The electronic structure changes in substituted nucleobases are discussed on the basis of photoelectron spectroscopic data. The electronic structure data are compared with structure-activity relationships regarding enzyme inhibition and complex formation. The electronic structure data give some insight into the nature of binding between nucleobases' derivatives and different enzymes whose activity they inhibit.     

Electronic structure of ZrCuSiAs and ZrCuSiP by X-ray photoelectron and absorption spectroscopy

The electronic structures of quaternary pnictides ZrCuSiPn (Pn=P, As) were analyzed by X-ray photoelectron spectroscopy (XPS) and X-ray absorption near-edge spectroscopy (XANES). Shifts in the core-line XPS and the XANES spectra indicate that the Zr and Cu atoms are cationic, whereas the Si and Pn atoms are anionic, consistent with expectations from simple bonding models. The Cu 2p XPS and Cu L-edge XANES spectra support the presence of Cu¹⁺. The small magnitudes of the energy shifts in the XPS spectra suggest significant covalent character in the Zr-Si, Zr-Pn, and Cu-Pn bonds. On progressing from ZrCuSiP to ZrCuSiAs, the Si atoms remain largely unaffected, as indicated by the absence of shifts in the Si 2p_3/2 binding energy and the Si L-edge absorption energy, while the charge transfer from metal to Pn atoms becomes less pronounced, as indicated by shifts in the Cu K-edge and Zr K, L-edge absorption energies. The transition from two-dimensional character in LaNiAsO to three-dimensional character in ZrCuSiAs proceeds through the development of Si-Si bonds within the [ZrSi] layer and Zr-As bonds between the [ZrSi] and [CuAs] layers.     

Electronic structure of monosubstituted benzenes and X-ray emission spectroscopy

The electronic structure of the phenol molecule in the gas phase was studied by X-ray emission spectroscopy (using the O-Kα and C-Kα spectra). MNDO calculations were performed, which made it possible to construct theoretical spectra and interpret experimental spectra. The structure of the molecular orbitals of phenol was compared with those of benzene and water. The π-interaction of the phenyl fragment with the oxygen-containing substituent was investigated. The contribution of the 2p atomic orbital of the oxygen atom to the π-HOMO of phenol is considerably less than that to lower-lying orbitals. For Part 3, see Ref. 1. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 12, pp. 2187–2193, December, 1997.     

Electronic structure of monosubstituted benzenes and X-ray emission spectroscopy

The electronic structure of the benzaldehyde molecule has been studied by X-ray emission spectroscopy. The gas-phase O-K- and C-K-spectra of this compound have been obtained. MNDO quantum-chemical calculations have been carried out. The structure of the MO's of benzaldehyde has been compared with those of benzene and formaldehyde molecules. The character of the p-p interaction of the phenyl and formyl fragments has been considered. The contribution of the latter to the highest occupied molecular orbitals of the-system has been shown to be small.Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 6, pp. 1033–1037, June, 1994.     

Electronic structure of monosubstituted benzenes and X-ray emission spectroscopy

The electronic structure of fluorobenzene was investigated by X-ray emission spectroscopy (using the F−Kα- and C−Kα-spectra) and quantum-chemical MNDO calculations. Molecular orbitals of fluorobenzene were compared with those of benzene and hydrogen fluoride. The P_π−p_π-interaction between the phenyl ring and the fluorine atom in the fluorobenzene molecule is weak for both the outer and inner π levels. For Part 2, see Ref. 1. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 8, pp. 1454–1460, August, 1997.     

Examination of the electronic structure of gaseous sulfur fluorides by soft X-ray spectroscopy

X-ray absorption spectra in the region of the L edge of S are reported for SF₄ and SF₆. These are interpreted in terms of transitions from the L sublevels of S to free MO [molecular absorption mechanism]. A semiempirical electron-structure calculation is reported for SF₆. The bond types are discussed.     

Electronic structure of Ni complexes by X-ray resonance Raman spectroscopy (resonant inelastic X-ray scattering)

The potential of 1s2p resonant inelastic (Raman) X-ray scattering (RIXS) is demonstrated for a series of Ni coordination complexes. In this technique, incident and scattered photon energies lie in the hard X-ray range (>5 keV). The 1s2p RIXS contour plots provide information that is complementary to K-edge and L-edge spectroscopy. RIXS spectroscopy promises to be a valuable probe of electronic structure     

Electronic structure of transition metal-cysteine complexes from X-ray absorption spectroscopy

The electronic structures of HgII, NiII, CrIII, and MoV complexes with cysteine were investigated by sulfur K-edge X-ray absorption near-edge structure (XANES) spectroscopy and density functional theory. The covalency in the metal-sulfur bond was determined by analyzing the intensities of the electric-dipole allowed pre-edge features appearing in the XANES spectra below the ionization threshold. Because of the well-defined structures of the selected cysteine complexes, the current work provides a reference set for further sulfur K-edge XAS studies of bioinorganic active sites with transition metal-sulfur bonds from cysteine residues as well as more complex coordination compounds with thiolate ligands.     

Electronic excitation energy transfer between nucleobases of natural DNA

Transfer of the electronic excitation energy in calf thymus DNA is studied by time-resolved fluorescence spectroscopy. The fluorescence anisotropy, after an initial decay starting on the femtosecond time scale, dwindles down to ca. 0.1. The in-plane depolarized fluorescence decays are described by a stretched exponential law. Our observations are consistent with one-dimensional transfer mediated by charge-transfer excited states.     

Electronic structure of calix[4]arene thioethers and their complexes with palladium,as studied by X-ray emission spectroscopy,X-ray photoelectron spectroscopy,and quantum chemistry

The charge state of calix[4]arene thioethers and their complexes with palladium was studied by X-ray emission spectroscopy and X-ray photoelectron spectroscopy. Experimental data were compared with the results of quantumchemical calculations. The involvement of the sulfur lone electron pairs in the coordination to Pd atoms causes a decrease in the energies of the corresponding MOs having contributions from the sulfur 3p AOs and, consequently, a decrease in the intensity of the maximum A on going from the S(Kβ) spectra of free ligands to the spectra of complexes. The binuclear nature of the complexes does not lead to the onset of significant additional interactions between two metal centers.     

Electronic structure of molecules of substituted benzenes by X-ray spectroscopy. I. Nitrobenzene

Institute of Inorganic Chemistry, Academy of Sciences of the USSR, Siberian Branch. Institute of Organic Chemistry, Academy of Sciences of the USSR, Siberian Branch. Translated from Zhurnal Strukturnoi Khimii, Vol. 28, No. 5, pp. 73–80, September–October, 1987.     

X-ray induced damage in DNA monitored by X-ray photoelectron spectroscopy

In this work, the chemical changes in calf thymus DNA samples were analyzed by X-ray photoelectron spectroscopy (XPS). The DNA samples were irradiated for over 5 h and spectra were taken repeatedly every 30 min. In this approach the X-ray beam both damages and probes the samples. In most cases, XPS spectra have complex shapes due to contributions of C, N, and O atoms bonded at several different sites. We show that from a comparative analysis of the modification in XPS line shapes of the C 1s, O 1s, N 1s, and P 2p peaks, one can gain insight into a number of reaction pathways leading to radiation damage to DNA.     

Noncovalent interactions in paired DNA nucleobases investigated by terahertz spectroscopy and solid-state density functional theory

Cocrystallized adenine and thymine derivatives, along with the pure monomeric crystals, were investigated by terahertz spectroscopy and solid-state density functional theory (DFT). The methylated nucleobase derivatives crystallize in planar hydrogen-bonded adenine-thymine pairs similar to the manner found in DNA. The spectra obtained for 1-methylthymine, 9-methyladenine, and the 1:1 cocrystal in the range of 10-100 cm(-1) clearly demonstrate that absorptions in this spectral range originate from the uniquely ordered assembly and the intermolecular interactions found in each individual crystal system. The quality of spectral reproduction for the DFT simulations of each system was clearly improved by the inclusion of an empirical correction term for London-type dispersion forces to the calculations. Notably, it was found that these weak dispersion forces in the adenine-thymine cocrystal were necessary to produce a properly converged crystal structure and meaningful simulation of the terahertz vibrational spectrum.     

Quantitative characterization of DNA films by X-ray photoelectron spectroscopy

We describe the use of self-assembled films of thiolated (dT)25 single-stranded DNA (ssDNA) on gold as a model system for quantitative characterization of DNA films by X-ray photoelectron spectroscopy (XPS). We evaluate the applicability of a uniform and homogeneous overlayer-substrate model for data analysis, examine model parameters used to describe DNA films (e.g., density and electron attenuation length), and validate the results. The model is used to obtain quantitative composition and coverage information as a function of immobilization time. We find that when the electron attenuation effects are properly included in the XPS data analysis, excellent agreement is obtained with Fourier transform infrared (FTIR) measurements for relative values of the DNA coverage, and the calculated absolute coverage is consistent with a previous radiolabeling study. Based on the effectiveness of the analysis procedure for model (dT)25 ssDNA films, it should be generally valid for direct quantitative comparison of DNA films prepared under widely varying conditions.     

High-resolution soft X-ray photoelectron spectroscopy of liquid water

High-resolution soft X-ray photoelectron spectra of liquid water (H(2)O and D(2)O) were measured using a liquid beam photoelectron spectrometer. The 1a(1) (O1s) band and the lowest valence 1b(1) band had single peaks, which is not consistent with the split 1b(1)→ 1a(1) of the X-ray emission band of liquid water if the splitting is assumed to originate from level shifts in two different hydrogen bonding structures. The second valence 3a(1) band of liquid water exhibited a flat top implying that two bands exist underneath a broad feature, which is similar to the case of the 3a(1) band of amorphous ice. The energy splitting between the two 3a(1) bands is estimated to be 1.38 eV (H(2)O) and 1.39 eV (D(2)O). Ab initio calculations suggest that the large splitting of the 3a(1) band is characteristic of water molecules that function as both proton donor and acceptor. The overall result is consistent with the conventional model of a tetrahedral hydrogen-bonding network in liquid water.     

Electronic excitations in synthetic eumelanin aggregates probed by soft X-ray spectroscopies

Electronic excitations of condensed phase eumelanin aggregates are investigated with soft X-ray spectroscopies. Resonant photoemission data indicate that mechanisms of charge delocalization may occur when electrons are excited about 3 eV above the first unoccupied electronic level. An average, lower limit value of 1.6 fs was estimated for the lifetime of the excited C 1s-pi* states.     

Electronic structure of N,N-dimethylnitramine and N,N-dimethylnitrosamine from X-ray and UV electron spectroscopy

The electronic structure of N,N-dimethylnitranine. (CH₃)₂NNO₂, and N,N,-dimethylnitrosamine, (CH₃)₂NNO, has been investigated through the use of electron spectroscopy and quantum chemical methods. Experimentally, the electron spectra of (CH₃)₂NNO₂ and (CH₃)₂NNO were measured in the valence region on the gas phase molecules using UV (HeI and He II) radiation and in the valence and core regions on the solid materials (frozen at 170 K) using X-radiation (AlK_α). Theoretically, the results of INDO and MWH Extended Hucket MO calculations are used for spectral interpretation. The semi-empirical potential model of Ellison is used for predicting is chemical shifts. The results of this investigation exemplify how the UV and X-ray electron spectroscopy techniques are symbiotic and how application of the two techniques along with the use of quantum chemical methods provide unique information about electronic structures.     

Electronic structure of guanidine and its derivatives from X-ray photoelectron spectroscopy and density functional theory studies

Electronic structure of guanidine, diphenylguanidine, their protonated forms, and guanidinium chloride have been studied by X-ray photoelectron spectroscopy and quantum-chemical modeling. From the derived geometry parameters and electronic structure, the effect of protonation on localization of the electron density has been revealed. The lines in the valence region of the X-ray photoelectron spectra have been assigned.     

Direct observation of defect levels in InN by soft X-ray absorption spectroscopy

We have used synchrotron-based near-edge X-ray absorption fine structure (NEXAFS) spectroscopy to study the electronic structure of nitrogen-related defects in InN(0001). Several defect levels within the band gap or the conduction band of InN were clearly resolved in NEXAFS spectra around the nitrogen K-edge. We attribute the level observed at 0.3 eV below the conduction band minimum (CBM) to interstitial nitrogen, the level at 1.7 eV above the CBM to antisite nitrogen, and a sharp resonance at 3.2 eV above the CBM to molecular nitrogen, in full agreement with theoretical simulations.