Electronic Structure of the Nucleobases

Abstract

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.

X-ray Absorption Spectroscopy of the Nucleotide Bases at the Carbon, Nitrogen, and Oxygen K-Edges

“…Peaks c and d are due to transitions from the 1s levels of C1 and C3, respectively, into the LUMO/ LUMO+1. Note that this assignment partly agrees with that proposed by MacNaughton et al 18 (the LUMOs of A and G were referred to as 7a′ and 8a′, respectively). Note also that we do not observe a π*(CdC) peak at ∼285.0 eV for both A and G in contrast to MacNaughton et al 18 and Samuel et al, 22 who used a similar sample preparation procedure and the same acquisition mode as in our work.…”

“…Note that this assignment partly agrees with that proposed by MacNaughton et al 18 (the LUMOs of A and G were referred to as 7a′ and 8a′, respectively). Note also that we do not observe a π*(CdC) peak at ∼285.0 eV for both A and G in contrast to MacNaughton et al 18 and Samuel et al, 22 who used a similar sample preparation procedure and the same acquisition mode as in our work. Since both StoBe and GSCF3 codes do not gives any peak at this particular energy for A and G, 18 it presumably corresponded to contamination.…”

“…[12][13][14] NEXAFS spectra of the nucleobases, nucleosides, nucleotides, and oligonucleotides measured with various NEXAFS detection techniques (i.e., electron yield or fluorescence yield) on differently prepared samples (e.g., thin evaporated or solution-cast films or polycrystalline powders) have been reported by several groups. [15][16][17][18][19][20][21][22][23][24] In particular, MacNaughton et al 18 reported a very detailed analysis of the NEXAFS spectra of four nucleotide bases occurring in DNA, viz., cytosine, thymine, adenine, and guanine, measured on pristine powder samples using the total fluorescence yield mode. Since fluorescence yield NEXAFS on thick concentrated samples is known to suffer from selfabsorption effects, their analysis was limited to the narrow π*-resonances below the main ionization threshold.…”

X-ray Fluorescence Spectroscopy of Novel Materials

“…The biological materials and systems studied to date by x-ray emission spectroscopy include vitamin B 12 and its derivatives [97,98], hemoglobin [99], antioxidants (aspirin and paracetamol) [100], chitosan [101], nucleo-and DNA bases [102][103][104], dental substitute materials [105], and human teeth [100]. Figure 27 shows the C K x-ray emission spectra for enamel, a caries area, and an intermediate region [100].…”

Electronic structures of DNA molecules and their alignment control on Si(100) substrates with one–dimensional lattices

“…The expected advantages of applying DNA molecules for electronic devices are: (1) possibility to synthesize any DNA oligomers with various sizes ($nm-mm) and sequences of four bases, adenine (A), thymine (T), guanine (G), and cytosine (C), to create nanoscale shapes and patterns [3], (2) flexible design of electronic structures by controlling the size and sequence to obtain useful electronic properties such as one-dimensional electron transports and superlattice structures as can be seen in the semiconductor microelectronic devices obtained by band engineering technologies, and (3) possibility to develop a new microscopic technique for the determination of the sequence in DNA strands. The calculated energy levels of the four bases A, T, G, and C [4,5] are compared with the experimental spectra obtained by ultraviolet photoelectron spectroscopy (UPS) measurements. We also show the preliminary results of controlling the alignment of relatively large DNA molecules by using one-dimensional lattices formed on Si(1 0 0) substrates.…”