ABSTRACT
The radiation-induced decomposition of glycine is studied using a combination of near-edge X-ray absorption fine structure (NEXAFS) measurements and DFT calculations. The measured spectra show strong dose- or time-dependent effects consistent with a complex, multistep decomposition. Principal component analysis was used to determine the number of distinct molecules that were needed to explain the observed changes in the measured spectra, and the emerging absorption features are assigned to various product molecules through comparison with simulated spectra of several model compounds. It is clear from the experiment that the major effect of soft X-ray irradiation is the fragmentation of the molecule, primarily at the carbonyl sites. Peptide formation is shown to occur under irradiation; a condensation reaction initiated by the removal of a carbonyl oxygen is the proposed mechanism. This study utilizes a novel approach to the study of radiation damage that can occur during measurements and suggests that it may be possible to use simulated model spectra to correct for these effects in measured spectra.
Subject(s)
Glycine/chemistry , Radiation , Absorption , Quantum Theory , Spectrum AnalysisABSTRACT
We present a comparison between experimental and theoretical X-ray absorption spectroscopy (XAS) and X-ray emission spectroscopy (XES) of 5-fluorouracil compounds, with an emphasis on the effects of the inclusion of nickel in the structure. By focusing on the 1s thresholds of carbon, nitrogen, oxygen, and fluorine it was possible to provide a complete picture of the occupied and unoccupied partial density of states of the 5-fluorouracil systems. Spectra calculated using density functional theory are compared to experimental results. Most experimental results agree well with our theoretical calculations for the XAS and XES of the compounds. All spectral features are assigned. Our results reveal that the nickel in the compound is coordinated with the nitrogen sites of the 5-fluorouracil ligands.
Subject(s)
Antimetabolites, Antineoplastic/chemistry , Chemistry, Physical/methods , Fluorouracil/chemistry , Carbon/chemistry , Chemistry, Pharmaceutical/methods , Electronics , Electrons , Fluorine/chemistry , Models, Molecular , Molecular Conformation , Nitrogen/chemistry , Oxygen/chemistry , Spectrometry, X-Ray Emission/methods , Spectrophotometry/methods , X-RaysABSTRACT
We present experimental and theoretical evidence that varying the local environment and physical structure of dried DNA has a direct impact on its electronic structure. By preparing samples of DNA in various solutions, it was possible to alter the type of ions present during the production of the DNA samples. These variations resulted in differences in the local chemical environment of the dried DNA molecules. X-ray absorption spectroscopy (XAS) and X-ray emission spectroscopy (XES) were used to probe the variations in the electronic structure of DNA samples. DFT calculations of a stack of 10 adenine (A)-thymine (T) nucleobase pairs show that slight structural variations in stacking height have a direct influence on the electronic structure and result in changes to the HOMO-LUMO gap. The effects of these differences in the local environment on the electronic structure are discussed and are related to the results of conductivity measurements of DNA.
Subject(s)
DNA/chemistry , Electrons , Models, Chemical , Nucleic Acid Conformation , Quantum Theory , Sensitivity and Specificity , Spectrum Analysis/methods , X-RaysABSTRACT
A combination of soft X-ray absorption spectroscopy (XAS) measurements and StoBe density functional theory (DFT) calculations has been used to study the electronic structures of the ferrocene-labeled peptides Fc-Pro(n)-OBz (n = 1-4). Excellent agreement between the measured and the simulated data is observed in all cases, and the origin of all major spectral features was assigned. The breaking of the degeneracy of the ferrocene 3e(2u)-like unoccupied molecular orbital under the influence of a substituent attached to a Cp ring was observed experimentally. The influence of the bonding environment on the O 1s and N 1s XAS spectra was examined. A corrected assignment of one of the major features in the Fe 2p XAS spectra of ferrocene is proposed and supported by the DFT simulations, as well as the measured spectra.
