Experimental and Theoretical Investigation of the ... - ACS Publications

18180

J. Phys. Chem. B 2006, 110, 18180-18190

Experimental and Theoretical Investigation of the Electronic Structure of 5-Fluorouracil Compounds J. B. MacNaughton,*,† R. G. Wilks,† J. S. Lee,‡ and A. Moewes† Department of Physics and Engineering Physics, UniVersity of Saskatchewan, 116 Science Place, Saskatoon, Saskatchewan S7N 5E2, Canada, and Department of Biochemistry, UniVersity of Saskatchewan, 107 Wiggins Road, Saskatoon, Saskatchewan S7N 5E5, Canada ReceiVed: March 13, 2006; In Final Form: July 30, 2006

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.

1. Introduction The biological activity of fluorine-substituted pyrimidine molecules, such as 5-fluorouracil (5FU), allows them to be effectively used as active chemotherapeutic agents.1 5FU interferes with nucleoside metabolism and can be incorporated into RNA and DNA. It has been found that these agents have the ability to bind to metal ions and can combine with tissues through the interaction with metals.2 This ability has led to a great deal of interest in the study of the physical structure and binding sites of 5FU complexes combined with transition metal ions, with the goal of understanding their role in biochemical reactions and their function as anticancer drugs.2,3 The 5FU structure consists of a heterocyclic aromatic organic compound, similar to that of the pyrimidine molecules for DNA and RNA, which include cytosine, thymine, and uracil. Understanding the physical and electronic structures of biomaterials is becoming increasingly important, as the desire to build devices on the nanoscale shifts focus to molecular electronics research. DNA is an attractive choice for use in this industry because of its self-assembly and molecular recognition properties. However, the results of experiments investigating the conductivity of DNA are often contradictory, with different studies suggesting that DNA has electrical properties ranging from insulating4-7 to semiconducting8-10 to highly conductive11 to superconducting12 behavior. The large number of atoms in the molecule and the interactions of DNA with its surrounding environment create considerable challenges when designing theoretical and experimental methods to provide insight into its electronic structure. In supplement to the debate concerning the electron transport properties of DNA, attempts have been made to improve the conductivity of DNA by integrating metal ions into the structure.13 With a deposit of silver atoms along the helical structure * Corresponding author. Tel.: +306-966-6380. Fax: +306-966-6400. E-mail: [email protected] (J. B. MacNaughton). † Department of Physics and Engineering Physics. ‡ Department of Biochemistry.

of DNA, the conductivity can be improved.4 However, this process renders the desirable self-assembly and molecular recognition properties of the DNA helix essentially unrecoverable. Incorporating metal directly into the structure may provide a means of introducing a more conductive element while still preserving these valuable properties of the DNA helix. Converting B-DNA to (X)‚M-DNA by the addition of divalent metal ions (Zn2+, Co2+, and Ni2+) at pH values above 8.5 improves the electron transport properties and is a reversible process.14,15 The electronic structure of complicated biomaterials such as DNA and metallic DNA systems can be examined using a building block approach. We have previously used soft X-ray spectroscopy in combination with Hartree-Fock and density functional theory simulations to study the electronic structure of the nucleobases of DNA.16 A systematic approach to understanding the complicated electronic structure of metallic DNA systems is to first examine the electronic structures of smaller components in the presence of transition metal ions. Soft X-ray absorption (XAS) and emission (XES) spectroscopy provide valuable information about a molecule’s unoccupied and occupied partial densities of states, respectively. Below we present the first comprehensive study of the electronic structure of 5FU compounds. This study includes experimental soft X-ray absorption and emission spectra for the C, N, O, and F edges compared to spectra simulated using density functional theory (DFT). The main transitions in the experimental XAS and XES spectra are identified using the results of calculations. The physical structure of the 5FU compound in the presence of nickel ions is discussed. 2. Sample Preparation Samples of deoxyribose-5-fluorouracil (d5FU) and (Ni)‚ deoxyribose-5-fluorouracil ((Ni)‚d5FU) were prepared in solution, then dried using lyophilization, and measured in powder form. A 100 mM solution of d5FU was prepared and divided. The (Ni)‚d5FU sample was prepared by the addition of 100 mM NaOH to the d5FU solution to remove the imino proton (pH 8.5) and then combining with 50 mM NiCl2. The intention

10.1021/jp061543j CCC: $33.50 © 2006 American Chemical Society Published on Web 09/02/2006

Electronic Structure of 5-Fluorouracil Compounds

J. Phys. Chem. B, Vol. 110, No. 37, 2006 18181

Figure 1. Molecular structures of the four 5FU structures: (a) 5-fluorouracil (5FU), (b) deoxyribose-5-fluorouracil (d5FU), (c) model of 5-flurouracil with nickel bonded to nitrogen ((Ni-N)‚5FU), and (d) model of 5-fluorouracil with nickel bonded to oxygen ((Ni-O)‚5FU).

TABLE 1: Geometry of 5FU Compounds Optimized by StoBe bond lengtha (Å) CsC CdC CsN CsF CdO CsO CsH NsH NsNi OsNi NsC (sugar) CsO (sugar) CsC (sugar) CsH (sugar) OsH (sugar) a

5FU

d5FU

(Ni-N)‚5FU

1.390 1.387 1.355 1.230 1.207

1.458 1.355 1.399 1.353 1.231

1.429 1.364 1.385 1.353 1.224

1.052 0.969

1.090 1.024

1.092 1.020 1.898

(Ni-O)‚5FU 1.399 1.395 1.352 1.226 1.266 1.090 1.027 1.820

1.501 1.436 1.533 1.106 0.979

Bond length is averaged when there are multiple occurrences.

was to prepare these samples under conditions similar to those used in the preparation of metallic DNA, where the metal ions are predicted to interact with the nitrogen atoms in the nucleobases.14 The nucleoside was purchased from Sigma, and the metal chloride salt was obtained from Aldrich.

Figure 2. Carbon 1s soft X-ray absorption (XAS) spectra including (a) d5FU experiment compared to theoretical spectra for 5FU, d5FU, and the deoxyribose and ring components of d5FU and (b) (Ni)‚d5FU experiment compared to theoretical spectra for (Ni-N)‚5FU, (Ni-N)‚ 5FU + deoxyribose ((Ni-N)‚d5FU), (Ni-O)‚5FU, and (Ni-N)‚5FU + deoxyribose ((Ni-O)‚d5FU). Experimental spectra are displayed with black lines and calculated spectra are shown with gray lines. An offset for the y-scale has been included for clarity.

sensitive multichannel detector. The details of this endstation are described elsewhere.17 Total experimental resolution in the KR X-ray emission region is 0.4 eV for carbon, 0.75 eV for nitrogen, 1.2 eV for oxygen, and 1.7 eV for fluorine (all full width at half-maximum (fwhm)). All absorption and emission spectra are normalized to the number of photons falling on the sample, monitored by a highly transparent gold mesh. Energy calibration was performed using measurements of reference samples and shifting the energy using values found in the literature. For these calibrations, highly oriented pyrolytic graphite18 was used for carbon edge, h-BN19 was used for the nitrogen edge, TiO220 was used for the oxygen edge, and CaF221 was used for the fluorine edge. 4. Calculations

3. Experimental Section The soft X-ray spectroscopic measurements were performed at Beamline 8.0.1 at the Advanced Light Source synchrotron at the Lawrence Berkeley National Laboratory. The X-ray absorption spectra were measured in total electron yield (TEY) mode for the carbon, nitrogen, and fluorine edges and total fluorescence yield (TFY) for the oxygen edge. The resolving power E/∆E for the absorption spectra is about 5000 for the carbon, nitrogen, oxygen, and fluorine edges. For the XES spectra, the emitted radiation is partially collected in a Rowland circle-type spectrometer with spherical gratings and recorded with an area-

Soft X-ray spectra were simulated using the commercially available StoBe software.22 To analyze the electronic structure of molecules, the program uses a linear combination of Gaussian type orbitals to form self-consistent solutions of the KohnSham DFT equations. Triple-ζ plus valence polarization (TZVP) Huzinaga orbital basis sets and A5 auxiliary basis sets derived from the TZVP basis sets were used in this study.23 The calculations of the absorption spectra use a combination of the transition potential method and a double basis set technique integrated into density functional theory. In this approach, the core electron undergoing the excitation is replaced by a half-

18182 J. Phys. Chem. B, Vol. 110, No. 37, 2006

MacNaughton et al.

TABLE 2: Assignment of Spectral Features for the C 1s Absorption Data 5FU

1 2 3

4

d5FU

transitiona

oscillator strength (×10-3)

C3 f Lb C1 f L C2 f L C1 f L + 1 C2 f L + 1 C2 f L + 2 C3 f L + 2 C4 f L C4 f L + 1 C1 f L + 2 C1 f L + 3 C2 f L + 4 C4 f L + 2

9.166 9.874 4.728 2.365 2.792 5.913 2.569 12.82 2.299 0.114 0.782 0.193 0.066

1 2

3

4

(Ni-N)‚5FU

transition


C4 f L C9 f L C2 f L C3 f L C4 f L + 1 C4 f L + 2 C4 f L + 3 C7 f L C9 f L + 1 C1 f L C2 f L + 1 C2 f L + 2 C2 f L + 3 C3 f L + 1 C3 f L + 2 C2 f L + 3 C5 f L C5 f L + 1 C5 f L + 2 C6 f L C6 f L + 1 C7 f L + 1 C8 f L + 2 C9 f L + 2 C9 f L + 3 C9 f L + 4 C1 f L + 3 C1 f L + 4 C7 f L + 2 C7 f L + 3 C7 f L + 4 C8 f L + 3 C8 f L + 4

0.244 18.01 0.005 0.267 1.106 0.640 2.675 19.12 0.195 0.186 7.943 2.832 0.275 3.388 1.595 2.606 8.217 0.185 4.118 23.21 5.579 4.404 14.33 3.685 1.720 0.089 4.624 9.185 1.128 0.191 0.173 0.419 0.042

1

2

3

4

(Ni-O)‚5FU

transition


C2 f L C3 f L C3 f L + 1 C6 f L C7 f L C7 f L + 1 C1 f L + 1 C2 f L + 1 C3 f L + 2 C4 f L C5 f L + 1 C6 f L + 1 C7 f L + 2 C8 f L C1 f L + 2 C1 f L + 3 C2 f L + 2 C2 f L + 3 C2 f L + 4 C3 f L + 4 C4 f L + 1 C4 f L + 2 C5 f L + 2 C5 f L + 3 C6 f L + 2 C6 f L + 3 C6 f L + 4 C7 f L + 4 C8 f L + 1 C8 f L + 2 C4 f L + 4 C8 f L + 4

0.174 0.028 17.57 0.175 0.028 17.57 17.84 6.139 0.118 0.427 17.84 6.138 0.118 0.427 0.142 5.169 0.275 9.321 13.15 5.183 0.168 27.34 0.142 5.168 0.276 9.320 13.15 5.184 0.168 27.34 0.005 0.005

1 2

3

4

transition


C3 f L C1 f L C2 f L C3 f L + 1 C5 f L C6 f L C7 f L + 1 C1 f L + 2 C1 f L + 3 C1 f L + 4 C2 f L + 2 C2 f L + 3 C2 f L + 4 C4 f L C4 f L + 1 C5 f L + 2 C5 f L + 3 C5 f L + 4 C6 f L + 2 C6 f L + 3 C6 f L + 4 C8 f L C8 f L + 1 C4 f L + 3 C4 f L + 4 C8 f L + 3 C8 f L + 4

15.63 15.97 6.228 0.477 15.97 6.228 0.477 4.252 0.042 0.008 7.263 9.795 2.676 19.02 9.988 4.252 0.042 0.008 7.263 9.795 2.675 19.02 9.988 0.188 0.002 0.188 0.002

a Transitions from core level in labeled atom (labels from Figure 1) to given unoccupied state. Boldface entries correspond to transitions into π-like orbitals and lightface entries correspond to transitions into σ-like orbitals. b L ) LUMO (lowest unoccupied molecular orbital).

occupied core hole.24 The excited state orbitals are calculated, and the probabilities for transitions between the core and unoccupied levels are determined. The calculated transitions were convoluted with a series of Gaussian functions having widths of 0.7 eV (fwhm) up to the ionization potential and then linearly increasing to 4.0 eV (fwhm) over the next 10 eV. These line widths were chosen to correspond to the experimentally observed results. All nonresonant X-ray emission spectra for the nucleobases were calculated using the StoBe code. The valence-core level transitions in these calculations are based on the calculated ground-state Kohn-Sham orbitals.25 The theoretical discrete emission rates for each constituent were Gaussian broadened with a constant line width of 1.0 eV (fwhm) for all edges. The broadened results from the individual atoms were summed into a final spectrum for each element and are compared to experimental results. The calculated emission spectra have been broadened less than the experimental results to ensure that the specific transitions that are occurring remain evident. Structural models for the calculations were created using the Spartan ‘04 program,26 and optimized using StoBe. Both 5-fluorouracil (5FU) and deoxyribose-5-fluorouracil (d5FU) were included to represent the molecule without the presence of transition metal ions. It has been suggested that the addition of Ni ions to 5FU structures will form a novel complex consisting of one metal ion for every two ligands, and this arrangement will be formed through the 4-keto group.2 Therefore, a model that includes two 5FU ligands bonded via nickel-oxygen bonds

((Ni-O)‚5FU) has been included in this study. However, the samples that were measured were specifically prepared at higherthan-usual pH in order to deprotonate the nitrogen sites and to consequently increase the likelihood of binding to that site. A model featuring two 5FU ligands joined through Ni-N bonds has also been included in this study ((Ni-N)‚5FU) to reflect the desired structure. The deoxyribose sugar has not been included in the metal-5FU complexes for simplicity; however a building block approach was utilized to add in the spectral contribution from the sugar afterward. This approach was justified by supplementary calculations that proved the spectrum of d5FU could be adequately modeled in this way. The molecular structures of the 5FU models are displayed in Figure 1. The numbering scheme of the atoms corresponds to the identifiers that will be used in the discussion of the simulated spectra. Table 1 includes bond length information for the 5FU models used for the simulations. In all cases, the theoretical spectra have been shifted in energy to align with the experimental data. For the XAS data, the calculated spectra were shifted to line up with the first low-energy absorption feature. The theoretical XES spectra were moved to align with the high-energy edge of the measured data. The minimum intensity value has been set to zero for all spectra. Since symmetry was not included in the calculations, the transitions up to the first five unoccupied orbitals in absorption are labeled with respect to the lowest unoccupied molecular orbital (LUMO) and the transitions in the emission process are labeled with respect to the highest occupied molecular orbital (HOMO).



Figure 4. Nitrogen 1s soft X-ray absorption (XAS) spectra including experimental results for d5FU and (Ni)‚d5FU compared to theoretical spectra for 5FU, d5FU, (Ni-N)‚5FU, and (Ni-O)‚5FU. Experimental spectra are displayed with black lines and calculated spectra are shown with gray lines. An offset for the y-scale has been included for clarity.

Figure 3. Nonresonant carbon KR emission (XES) spectra including (a) d5FU experiment compared to theoretical spectra for 5FU, d5FU, and the deoxyribose and ring components of d5FU, and (b) (Ni)‚d5FU experiment compared to theoretical spectra for (Ni-N)‚5FU, (Ni-N)‚ 5FU + deoxyribose ((Ni-N)‚d5FU), (Ni-O)‚5FU, and (Ni-N)‚5FU + deoxyribose ((Ni-O)‚d5FU). Experimental spectra are displayed with black lines and calculated spectra are shown with gray lines. An offset for the y-scale has been included for clarity.

5. Results and Discussion Figure 2 shows the carbon 1s XAS spectra for (a) d5FU measurements compared to calculated results for 5FU and d5FU and (b) (Ni)‚d5FU measurements compared to theoretical results for (Ni-N)‚5FU and (Ni-O)‚5FU. Although symmetry was not included in the calculations, it is assumed that the transitions that occur in these systems during the absorption process will be similar to those seen in the nucleobases of DNA. It is therefore assumed that transitions directly above the onset of absorption are to π* type orbitals and then shifting to transitions to σ* type orbitals as the excitation energy increases.16 The calculated molecular orbitals were visualized to determine whether the orbital has π- or σ-like symmetry. This information has been included in the transition tables in this study. The agreement between theoretical and experimental data is excellent in the region of the lower energy features that result from the excitation of the carbon 1s core electron to the π* unoccupied orbitals. The results of the StoBe calculations allow the origins of the prominent spectral features to be examined in detail. The origins of the numbered features in the StoBe spectra are outlined in Table 2. The contributing transitions for each labeled feature are described; the origin of each major transition occurring within (0.5 eV of the location of the number is included. The presence of the deoxyribose sugar in the structures increases the number of carbon atoms probed and provides a greater overlap of transitions occurring from the many

carbon atoms as shown in Table 2. Therefore, the site selectivity established in the carbon 1s XAS spectra of the nucleobase pyrimidines is not feasible in these systems.16 The symmetry in the structures of the (Ni-N)‚5FU and (Ni-O)‚5FU models leads to similar transitions and oscillator strengths for analogous sites. These symmetrical transitions are found for the C, N, O, and F absorption and emission processes. Although the four main carbon 1s absorption peaks found in the experimental spectra in Figure 2 are represented in the calculated results of 5FU, d5FU, (Ni-N)‚5FU, and (Ni-O)‚ 5FU, it is found that the inclusion of the deoxyribose sugar is important for the best agreement between experiment and theory. As seen in Figure 2a, when the d5FU calculation is split into contributions from the carbon atoms in the deoxyribose sugar and the carbon atoms in the ring structure, the spectral contributions are quite different. The onset of absorption for the sugar is 2.6 eV higher in energy than the onset for the ring. The intensities of the peaks in the d5FU theory correspond better to experiment than the simple 5FU structure. By adding the deoxyribose spectral component from the calculation of d5FU to the calculated spectra of (Ni-N)‚5FU and (Ni-O)‚5FU, we obtain the (Ni-N)‚d5FU and (Ni-O)‚d5FU spectra shown in Figure 2b. This results in improvement in the agreement between experiment and theory, particularly with the intensity of the fourth absorption feature. Comparing the experimental data for d5FU and (Ni)‚d5FU in parts a and b Figure 2, respectively, it is found that the inclusion of the Ni does not have a significant impact on the carbon spectra. This can also be said about the calculated C 1s XAS spectra, indicating that the Ni does not strongly interact with carbon in the structure of (Ni)‚d5FU. This is in agreement with what would be expected in either the (Ni-N)‚5FU or the (Ni-O)‚5FU model that was used in the calculations. Nonresonant carbon KR X-ray emission spectra of the 5FU compounds are displayed in Figure 3. Figure 3a displays the


MacNaughton et al.

TABLE 3: Assignment of Spectral Features for the C Kr Emission Data 5FU

1 2

3

4

d5FU

transitiona


Hb-14 f C2 H-14 f C3 H-14 f C1 H-12 f C2 H-10 f C3 H-12 f C3 H-14 f C4 H-6 f C1 H-7 f C1 H-4 f C3 H-7 f C4 H-8 f C4 H-9 f C4 H f C2 H f C3

438.9 324.8 346.6 469.2 373.9 303.3 330.1 637.9 304.5 471.6 229.7 308.1 354.4 625.0 272.1

1

2

3

4

(Ni-N)‚5FU

transition


H-28 f C3 H-27 f C5 H-29 f C8 H-26 f C9 H-24 f C1 H-26 f C1 H-20 f C2 H-13 f C4 H-14 f C4 H-15 f C4 H-20 f C5 H-10 f C3 H-7 f C4 H-8 f C4 H-9 f C4 H-12 f C5 H-18 f C6 H-19 f C6 H-16 f C7 H-8 f C9 H f C8 H f C9

256.7 276.9 337.0 211.5 205.5 192.8 186.1 203.2 254.8 253.8 219.0 213.7 267.6 200.8 262.1 200.9 256.5 255.9 335.9 430.1 595.1 207.9

1

2 3

4

(Ni-O)‚5FU

transition


H-35 f C2 H-35 f C3 H-32 f C6 H-34 f C6 H-25 f C3 H-17 f C1 H-19 f C1 H-13 f C3 H-14 f C3 H-20 f C4 H-17 f C5 H-19 f C5 H-13 f C7 H-14 f C7 H-20 f C8 H-3 f C2 H-4 f C2 H-3 f C6 H-4 f C6

182.2 176.8 180.1 180.4 194.2 252.2 190.4 226.6 253.4 230.4 211.6 226.6 255.2 225.0 223.9 281.5 249.9 307.0 229.0

1

2

3

4

transition


H-31 f C3 H-32 f C3 H-34 f C5 H-31 f C7 H-32 f C7 H-27 f C1 H-30 f C1 H-24 f C3 H-30 f C5 H-24 f C7 H-18 f C1 H-13 f C3 H-14 f C3 H-19 f C4 H-20 f C4 H-22 f C4 H-17 f C5 H-13 f C7 H-14 f C7 H-19 f C8 H-20 f C8 H-21 f C8 H-5 f C2 H-6 f C2 H-5 f C6 H-6 f C6

192.8 210.1 187.0 193.7 208.3 213.3 204.5 208.2 212.0 202.7 320.9 238.0 245.5 244.2 250.4 187.0 336.3 244.6 238.8 253.3 241.7 187.7 292.1 305.1 316.7 281.3

a Transitions from an occupied state to a core level in labeled atom (labels from Figure 1). Boldface entries correspond to transitions into π-like orbitals and lightface entries correspond to transitions into σ-like orbitals. b H ) HOMO (highest occupied molecular orbital).

TABLE 4: Assignment of Spectral Features for the N 1s Absorption Data 5FU

1 2 3

d5FU

transitiona


N1 f Lb N2 f L N1 f L + 2 N2 f L + 1 N2 f L + 2 N2 f L + 4

2.169 1.748 0.379 1.338 1.537 1.751

1 2 3

(Ni-N)‚5FU

transition


N1 f L N2 f L N1 f L + 1 N2 f L + 1 N1 f L + 2 N1 f L + 3 N1 f L + 4 N2 f L + 2 N2 f L + 3 N2 f L + 4

3.885 4.612 3.285 1.085 0.337 0.362 1.137 3.301 0.629 0.145

1 2 3

4

5

(Ni-O)‚5FU

transition


N1 f L N3 f L N1 f L + 1 N3 f L + 1 N1 f L + 2 N1 f L + 3 N2 f L + 1 N3 f L + 2 N3 f L + 3 N4 f L + 1 N1 f L + 4 N2 f L + 2 N2 f L + 3 N3 f L + 4 N4 f L + 2 N4 f L + 3 N2 f L + 4 N4 f L + 4

1.743 1.741 5.415 5.416 0.150 1.379 4.834 0.150 1.379 4.833 1.000 0.296 1.137 1.000 0.296 1.137 4.113 4.111

1

2

3

transition


N1 f L N1 f L + 1 N2 f L N3 f L N3 f L + 1 N4 f L N1 f L + 2 N1 f L + 3 N2 f L + 1 N2 f L + 2 N3 f L + 2 N3 f L + 3 N4 f L + 1 N4 f L + 2 N2 f L + 3 N2 f L + 4 N4 f L + 3 N4 f L + 4

3.738 0.310 3.112 3.738 0.310 3.112 1.213 3.027 0.091 2.364 1.213 3.027 0.091 2.364 1.360 0.009 1.360 0.009


experimental d5FU spectrum compared to calculations of 5FU and d5FU, while part b compares the theoretical predictions for the metal 5FU models to the (Ni)‚d5FU experimental spectrum. The excitation energy used for measuring these spectra was above the carbon 1s absorption edge, at 300 eV. Slight variations exist in the experimental spectra, reflecting differences in the occupied density of states of the molecules. Agreement between the experimental data and the StoBe simulations is quite good. The carbon emission consists of a large broad feature

that is the result of many transitions between the occupied states with p symmetry and the open K shells in the different carbon atoms. The calculation of the 5FU spectrum is more discrete and has sharper peaks due to significantly fewer carbon atoms involved in the calculation as compared to the other theoretical spectra. The addition of the spectral contribution of the sugar has less impact on the agreement between experiment and theory than with the absorption spectra, because the calculated XES for deoxyribose and the ring are found to be quite similar.


Figure 5. Nonresonant nitrogen KR emission (XES) spectra including experimental results for d5FU and (Ni)‚d5FU compared to theoretical spectra for 5FU, d5FU, (Ni-N)‚5FU, and (Ni-O)‚5FU. Experimental spectra are displayed with black lines and calculated spectra are shown with gray lines. An offset for the y-scale has been included for clarity.

Therefore, the main effect of the inclusion of the sugar is to broaden the key emission features by including transitions from the occupied orbitals to a greater number of carbon core levels. The main transitions, with oscillator strengths greater than 180 × 10-3, associated with the numbered features in Figure 3, are identified in Table 3. Figure 4 displays the nitrogen 1s X-ray absorption spectra of the 5FU compounds. Although many of the main features are represented in the theory, some variations in peak intensity and location occur between the experimental and theoretical spectra. A possible source of deviation is that the calculations were performed for gas-phase molecules that may not reflect the conformation of the powdered samples that were measured. These variations in the nitrogen spectra were also found for the nucleobases and were attributed to intermolecular effects resulting from the involvement of the nitrogen atoms in the intermolecular hydrogen bond network.16 Transitions into the various π* levels of the different nitrogen sites produce the multiple preedge peaks seen in the spectra. The excitations to the multiple σ* orbitals dominate the broader features seen at higher energies. The main transitions corresponding to the regions ((0.5 eV) under the numbers in Figure 4 are included, along with their oscillator strengths, in Table 4. The inclusion of the Ni has a significant effect on the spectra of the nitrogen edge. A main difference between the experimental spectra of d5FU and (Ni)‚d5FU in Figure 4 is the increase in the intensity of the lowest-energy π* feature. Comparing the experimental (Ni)‚d5FU spectrum to the simulated spectra of the (Ni-N)‚5FU and (Ni-O)‚5FU models is particularly important at the N and O edges, as it should provide insight into which structure is represented in the measured samples. For the nitrogen edge, the calculation of (Ni-N)‚5FU corresponds better to the experimental spectrum with both the


Figure 6. Oxygen 1s soft X-ray absorption (XAS) spectra including (a) d5FU experiment compared to theoretical spectra for 5FU, d5FU, and the deoxyribose and ring components of d5FU and (b) (Ni)‚d5FU experiment compared to theoretical spectra for (Ni-N)‚5FU, (Ni-N)‚ 5FU + deoxyribose ((Ni-N)‚d5FU), (Ni-O)‚5FU, and (Ni-N)‚5FU + deoxyribose ((Ni-O)‚d5FU). Experimental spectra are displayed with black lines and calculated spectra are shown with gray lines. An offset for the y-scale has been included for clarity.

location and intensity of the spectral features than the calculation of (Ni-O)‚5FU. In particular, the prominent feature seen near 404 eV in the simulated (Ni-O)‚5FU spectrum is absent from the measured spectrum. The spectra in Figure 4 signify that the nickel is coordinated with the nitrogen atoms rather than with the oxygen in the structure of (Ni)‚d5FU. This suggests that the synthesis procedure was successful in producing the desired (Ni-N)‚5FU structure. Figure 5 shows the nonresonant N KR X-ray emission spectra for the 5FU compounds with the corresponding theoretical spectra calculated using StoBe. The excitation energy used for the emission data was 417.7 eV. The nitrogen XES involves many different transitions from occupied levels occurring in the multiple nitrogen atoms in the molecules, as seen with the carbon emission. The difference in the shape of the low energy onset of the experimental emission spectra for d5FU and (Ni)‚ d5FU reveals that the inclusion of Ni has a significant effect on the nitrogen occupied states. All features in the experimental data are reasonably well predicted by the spectral simulations. The transitions that provide a major contribution (oscillator strengths greater than 350 × 10-3) to the labeled peaks in Figure 5 are shown in Table 5. The oxygen 1s X-ray absorption spectra for (a) d5FU experiment compared to calculated results for 5FU and d5FU and (b) (Ni)‚d5FU experiment compared to theoretical results for (Ni-N)‚5FU and (Ni-O)‚5FU are displayed in Figure 6. The sharper peaks located at lower energy are mainly from


MacNaughton et al.

TABLE 5: Assignment of Spectral Features for the N Kr Emission Data 5FU

1 2 3

4 5 6

d5FU

transitiona


Hb-16 f N1 H-16 f N2 H-17 f N2 H-14 f N1 H-14 f N2 H-15 f N2 H-11 f N1 H-12 f N1 H-13 f N1 H-13 f N2 H-6 f N2 H-3 f N1 H-2 f N2 H f N2

1102 500.2 746.6 549.1 727.4 865.6 430.7 654.1 942.8 895.1 516.2 1720 176.6 1107

1 2 3 4 5 6 7

(Ni-N)‚5FU

transition


H-34 f N1 H-30 f N1 H-30 f N2 H-26 f N1 H-25 f N2 H-26 f N2 H-15 f N2 H-8 f N1 H-4 f N2 H f N1

806.4 490.1 409.3 485.6 869.3 425.0 365.8 667.4 1595 1134

1

2

3

4

(Ni-O)‚5FU

transition


H-36 f N1 H-37 f N1 H-36 f N3 H-37 f N3 H-32 f N2 H-33 f N2 H-34 f N2 H-35 f N2 H-32 f N4 H-33 f N4 H-34 f N4 H-35 f N4 H-11 f N1 H-14 f N2 H-10 f N3 H-11 f N3 H-14 f N4 H-3 f N2 H-4 f N2 H-3 f N4 H-4 f N4

506.4 614.2 597.3 520.8 416.1 435.0 491.5 455.8 407.5 445.6 470.8 475.2 827.5 337.1 362.6 956.5 354.2 523.2 414.9 488.9 443.7

1

2

3

4

5

transition


H-37 f N1 H-38 f N1 H-37 f N3 H-38 f N3 H-33 f N2 H-34 f N2 H-35 f N2 H-36 f N2 H-33 f N4 H-34 f N4 H-35 f N4 H-36 f N4 H-28 f N1 H-29 f N1 H-31 f N1 H-32 f N1 H-31 f N2 H-32 f N2 H-28 f N1 H-29 f N1 H-31 f N1 H-32 f N1 H-31 f N4 H-32 f N4 H-9 f N1 H-10 f N1 H-9 f N3 H-10 f N3 H-5 f N2 H-6 f N2 H-5 f N4 H-6 f N4

560.1 550.0 561.0 549.2 384.1 367.9 399.7 395.6 382.9 369.0 402.3 393.0 407.8 379.1 382.1 416.2 534.4 494.2 407.4 379.4 381.3 417.1 536.4 492.3 876.3 834.5 874.4 836.3 489.7 457.3 485.6 461.2


TABLE 6: Assignment of Spectral Features for the O 1s Absorption Data 5FU

1 2 3 4

d5FU

transitiona


O1 f Lb O1 f L + 1 O2 f L O2 f L + 1 O1 f L + 2 O1 f L + 3 O2 f L + 2 O2 f L + 4

4.085 0.885 1.146 3.751 0.428 0.224 0.075 0.029

1 2 3

4

(Ni-N)‚5FU

transition


O3 f L O3 f L + 1 O4 f L O4 f L + 1 O1 f L + 1 O2 f L O2 f L + 1 O3 f L + 4 O4 f L + 3 O4 f L + 4 O5 f L O5 f L + 4

7.748 1.693 2.777 6.894 2.834 0.454 2.788 1.030 0.107 0.132 4.948 1.687

1

2

3

(Ni-O)‚5FU

transition


O1 f L O2 f L O3 f L O4 f L O1 f L + 2 O1 f L + 3 O2 f L + 1 O3 f L + 2 O3 f L + 3 O2 f L + 1 O1 f L + 4 O2 f L + 3 O3 f L + 4 O4 f L + 3

0.010 3.706 0.010 3.707 7.141 2.338 4.369 7.147 2.333 4.368 0.116 1.628 0.116 1.627

1

2

transition


O1 f L O1 f L + 1 O1 f L + 2 O2 f L O3 f L O3 f L + 1 O3 f L + 2 O4 f L O1 f L + 3 O1 f L + 4 O2 f L + 2 O2 f L + 3 O2 f L + 4 O3 f L + 3 O3 f L + 4 O4 f L + 2 O4 f L + 3 O4 f L + 4

0.841 7.998 0.737 5.860 0.841 7.998 0.737 5.860 0.084 0.002 1.315 1.706 0.024 0.084 0.002 1.315 1.706 0.024


transitions to the π* states, while the broader features at higher energy are the result of transitions to σ* states. Differences between the experimental results for d5FU and (Ni)‚d5FU indicate that there is a minor change in the electronic structure

of the oxygen when the Ni is added. The origins of the main transitions, corresponding to the regions ((0.5 eV) under the numbers in Figure 6, can be found along with their calculated oscillator strengths in Table 6.



Figure 8. Fluorine 1s soft X-ray absorption (XAS) spectra including experimental results for d5FU and (Ni)‚d5FU compared to theoretical spectra for 5FU, d5FU, (Ni-N)‚5FU, and (Ni-O)‚5FU. Experimental spectra are displayed with black lines and calculated spectra are shown with gray lines. An offset for the y-scale has been included for clarity.

Figure 7. Nonresonant oxygen KR emission (XES) spectra including (a) d5FU experiment compared to theoretical spectra for 5FU, d5FU, and the deoxyribose and ring components of d5FU and (b) (Ni)‚d5FU experiment compared to theoretical spectra for (Ni-N)‚5FU, (Ni-N)‚ 5FU + deoxyribose ((Ni-N)‚d5FU), (Ni-O)‚5FU, and (Ni-N)‚5FU + deoxyribose ((Ni-O)‚d5FU). Experimental spectra are displayed with black lines and calculated spectra are shown with gray lines. An offset for the y-scale has been included for clarity.

As was the case with the carbon spectra it is found that including the contribution of the deoxyribose sugar is important for the greatest agreement between experiment and theory. Figure 6a displays the calculation of d5FU broken down into the contributions from the deoxyribose oxygen and the oxygen atoms associated with the ring. The spectra of the sugar and the ring are significantly different, and the absorption onset for the sugar is 3.8 eV higher in energy than for the ring. The intensities of the peaks in the d5FU calculation correspond better to experiment than those in 5FU simulation. Adding the deoxyribose spectral component from the d5FU calculation to the calculated spectra of (Ni-N)‚5FU and (Ni-O)‚5FU results in the (Ni-N)‚d5FU and (Ni-O)‚d5FU spectra shown in Figure 6b. The addition of the spectra improves the agreement between experiment and theory in the broader σ*-type features. On comparison of the experimental (Ni)‚d5FU spectrum to the theoretical results, it is found that the calculation of (NiN)‚5FU corresponds better to the experimental spectrum than the calculation of (Ni-O)‚5FU. The (Ni-N)‚5FU calculation predicts a double peak structure at the onset of absorption, while the (Ni-O)‚5FU calculation predicts a single peak for the first main π* absorption feature. The experimental spectrum displays a broad onset peak, which corresponds more closely to the double peak onset structure predicted by the (Ni-N)‚5FU

Figure 9. Nonresonant fluorine KR emission spectra including experimental results for d5FU and (Ni)‚d5FU compared to theoretical spectra for 5FU, d5FU, (Ni-N)‚5FU, and (Ni-O)‚5FU. Experimental spectra are displayed with black lines and calculated spectra are shown with gray lines. An offset for the y-scale has been included for clarity.


MacNaughton et al.

TABLE 7: Assignment of Spectral Features for the O Kr Emission Data 5FU

1 2 3

d5FU

transitiona


Hb-7 f O2 H-8 f O2 H-5 f O1 H-6 f O1 H-4 f O2 H-1 f O1 H-2 f O1 H-3 f O1 H-1 f O2 H-2 f O2

1831 2658 796.6 2089 1538 4934 1640 2253 1744 4529

1

2

3

4

(Ni-N)‚5FU

transition


H-20 f O1 H-21 f O1 H-15 f O3 H-16 f O3 H-18 f O3 H-16 f O4 H-18 f O4 H-17 f O1 H-12 f O2 H-14 f O2 H-13 f O3 H-17 f O5 H-9 f O1 H-7 f O2 H-3 f O3 H-4 f O3 H-3 f O4 H-4 f O4 H-6 f O4 H-7 f O5 H-5 f O1 H-6 f O1 H-2 f O2 H f O3 H-1 f O3 H f O4 H-1 f O4 H-5 f O5 H-6 f O5

1106 998.0 507.7 3059 803.3 1297 2352 659.4 772.1 1861 1331 1144 2628 2110 1298 2025 2006 2393 2147 677.1 872.1 1883 5429 834.1 4794 1018 1548 3582 1942

1

2

3

(Ni-O)‚5FU

transition


H-18 f O1 H-20 f O1 H-21 f O1 H-25 f O2 H-29 f O2 H-18 f O3 H-20 f O3 H-21 f O3 H-25 f O4 H-28 f O4 H-29 f O4 H-13 f O1 H-14 f O1 H-17 f O2 H-19 f O2 H-13 f O3 H-14 f O3 H-17 f O4 H-19 f O4 H-3 f O1 H-5 f O1 H-6 f O1 H-7 f O1 H-9 f O2 H-10 f O2 H-11 f O2 H-12 f O2 H-3 f O3 H-5 f O3 H-6 f O3 H-7 f O3 H-9 f O4 H-10 f O4 H-11 f O4 H-12 f O4

1433 1831 782.2 1226 1165 1411 1858 772.3 811.1 609.6 773.8 811.7 753.3 849.0 1248 839.8 726.4 1289 822.3 945.9 1819 3078 1576 1467 1997 782.4 1602 960.1 1620 3291 1560 974.0 3004 1176 1066

1

2

3

transition


H-19 f O1 H-20 f O1 H-23 f O2 H-19 f O3 H-20 f O3 H-23 f O4 H-13 f O1 H-14 f O1 H-17 f O2 H-18 f O2 H-13 f O3 H-14 f O3 H-17 f O4 H-18 f O4 H-7 f O1 H-8 f O1 H-9 f O2 H-10 f O2 H-11 f O2 H-12 f O2 H-7 f O3 H-8 f O3 H-9 f O4 H-10 f O4 H-11 f O4 H-12 f O4

2247 2246 652.5 2266 2228 718.6 696.3 675.8 1635 938.7 689.7 682.2 913.8 1679 3099 3150 1684 859.1 2791 2877 3076 3175 942.4 1534 2833 2334


TABLE 8: Assignment of Spectral Features for the F 1s Absorption Data 5FU

transitiona 1 2 3

Lb

F1 f F1 f L+1 F1 f L+2 F1 f L+4

d5FU oscillator strength (×10-3) 0.657 0.789 9.634 0.073

1 2 3

(Ni-N)‚5FU

transition


F1 f L F1 f L+1 F1 f L+2 F1 f L+3 F1 f L+4

0.560 0.640 9.701 0.014 0.498

1

2

(Ni-O)‚5FU

transition


F1 f L F1 f L+1 F2 f L F2 f L+1 F1 f L+3 F1 f L+4 F2 f L+3 F2 f L+4

0.171 0.378 0.171 0.378 9.638 1.013 9.560 1.091

1 2

transition


F1 f L F2 f L F1 f L+2 F1 f L+3 F2 f L+2 F2 f L+3

0.359 0.359 0.846 8.873 0.846 8.873


calculation. This is further evidence that the Ni is bonded to nitrogen atoms rather than to the oxygen atoms in the structure of (Ni)‚d5FU. Figure 7 includes the results from nonresonant O KR X-ray emission measurements for the 5FU compounds. These emission spectra were measured with the excitation energy set at 552.9 eV. The oxygen emission results from transitions occurring from occupied states with p symmetry to the open K shells in the oxygen atoms. The inclusion of Ni into the d5FU structure does not have a major effect on the experimental spectra. Experi-

mental and theoretical agreement is quite good. The addition of the spectral contribution of the sugar improves the agreement between experiment and theory minimally since the calculations for the oxygen emission of the deoxyribose sugar and the ring are not significantly different. The spectra from both the (NiN)‚d5FU and (Ni-O)‚d5FU models are very similar in this case. Table 7 displays the labels for the most prominent transitions occurring in the oxygen emission process with oscillator strengths greater than 600 × 10-3, corresponding to the numbered peaks in Figure 7.



TABLE 9: Assignment of Spectral Features for the F Kr Emission Data 5FU

1 2 3 4 5

d5FU

transitiona


Hb-15 f F1 H-11 f F1 H-12 f F1 H-13 f F1 H-8 f F1 H-9 f F1 H-4 f F1 H-5 f F1 H-6 f F1 H f F1

3421 2147 4590 909.2 1281 6692 1880 9371 959.1 1840

1 2

3 4

5

(Ni-N)‚5FU

transition


H-29 f F1 H-30 f F1 H-23 f F1 H-24 f F1 H-25 f F1 H-26 f F1 H-18 f F1 H-19 f F1 H-21 f F1 H-8 f F1 H-9 f F1 H-10 f F1 H-11 f F1 H-12 f F1 H-13 f F1 H f F1

2311 779.1 1432 802.0 2857 474.4 646.6 5928 529.5 1276 420.8 1305 7254 645.0 920.2 1677

1

2

3

4

5

(Ni-O)‚5FU

transition


H-32 f F1 H-33 f F1 H-34 f F1 H-35 f F1 H-32 f F2 H-33 f F2 H-34 f F2 H-35 f F2 H-30 f F1 H-31 f F1 H-30 f F2 H-31 f F2 H-18 f F1 H-20 f F1 H-21 f F1 H-22 f F1 H-23 f F1 H-18 f F2 H-20 f F2 H-21 f F2 H-22 f F2 H-23 f F2 H-12 f F1 H-13 f F1 H-14 f F1 H-12 f F2 H-13 f F2 H-14 f F2 H-3 f F1 H-4 f F1 H-3 f F2 H-4 f F2

611.5 724.4 1765 1730 638.1 698.5 1800 1694 2319 2320 2403 2234 1147 814.8 1900 3189 3607 1152 807.1 1913 3546 3249 836.9 847.8 843.5 843.4 859.7 831.4 856.0 754.7 851.5 758.2

1

2

3

4

5

transition


H-35 f F1 H-36 f F1 H-35 f F2 H-36 f F2 H-25 f F1 H-26 f F1 H-28 f F1 H-29 f F1 H-31 f F1 H-32 f F1 H-25 f F2 H-26 f F2 H-28 f F2 H-29 f F2 H-31 f F2 H-32 f F2 H-21 f F1 H-22 f F1 H-23 f F1 H-24 f F1 H-21 f F2 H-22 f F2 H-23 f F2 H-24 f F2 H-15 f F1 H-16 f F1 H-15 f F2 H-16 f F2 H-5 f F1 H-6 f F1 H-5 f F2 H-6 f F2

1812 1806 1816 1802 1065 1056 1888 2271 729.2 524.1 1062 1059 1892 2266 730.0 523.8 3260 3276 1223 1201 3268 3268 1221 1203 5119 5118 5131 5107 937.1 919.0 934.7 921.4


The fluorine 1s X-ray absorption data for the 5FU compounds are displayed in Figure 8. The calculated fluorine spectra are the most discrete and contain the sharpest features compared to the other edges included in this study due to fewer sites. All calculated spectra are quite similar and represent the main features found in the experimental data. The main transitions corresponding to the regions ((0.5 eV) under the numbers in Figure 8 are labeled along with their oscillator strengths given from the StoBe program and can be found in Table 8. The experimental data for d5FU and (Ni)‚d5FU are very similar, with the exception of a π* type feature emerging around 680 eV after the inclusion of the Ni into the structure. This peak may reflect a delocalization of the bonding in the 5FU brought about by the presence of the metal, leading to a partial overlap of the single-bonded fluorine orbitals with an adjacent π* orbital. Alternatively, this spectral feature may be the result of intermolecular effects caused by the fluorine atom interacting with surrounding molecules in the powder sample. Figure 9 shows the results from nonresonant F KR X-ray emission measurements for the 5FU compounds. These emission spectra were measured with the excitation energy set at 732.5 eV. The measured emission features are more discrete than the carbon, nitrogen, and oxygen edges because there are fewer sites contributing to the emission process. The effects of the inclusion of Ni can be seen in the experimental data for d5FU and (Ni)‚ d5FU. The main emission feature has two peaks for d5FU, while this structure is not distinct for (Ni)‚d5FU. As with the oxygen emission, the spectra from both the (Ni-N)‚d5FU and (NiO)‚d5FU models are quite similar. Table 9 displays the labels

for the most prominent transitions with oscillator strengths greater than 400 × 10-3 occurring in the fluorine emission process, corresponding to the numbered peaks in Figure 9. 6. Conclusions Soft X-ray absorption spectroscopy and emission spectroscopy are used to study the electronic structures of d5FU and (Ni)‚d5FU. The experimental results are compared to calculated spectra of 5FU and d5FU, as well as to the (Ni-N)‚d5FU and (Ni-O)‚d5FU models. The spectral contribution of the deoxyribose sugar is found to be important at the C and O edges for improved agreement between experiment and theory. Spectral features are assigned in the XAS and XES spectra according to the calculations. The experimental and theoretical results for the 5FU compounds demonstrate each has a unique partial density of states for the carbon, nitrogen, oxygen, and fluorine sites. Our investigation was particularly focused on the effect of the addition of the Ni ion on the electronic structure and chemical bonding of the 5-fluorouracil compounds. In some cases the effect of the Ni addition is very weak (C edge), while in others it is prominent (N, O, and F edges). Better agreement between the experimental results for (Ni)‚d5FU and the calculations of the (Ni-N)‚5FU model indicate the nickel ions are coordinated with nitrogen in the structure of (Ni)‚d5FU. By probing the electronic density of states using our experimental techniques and combining with theoretical results, we have provided a full description of the electronic structure of the 5FU compounds.

18190 J. Phys. Chem. B, Vol. 110, No. 37, 2006 Acknowledgment. Funding by the Natural Sciences and Engineering Research Council of Canada (NSERC) and the Canada Research Chair Program is gratefully acknowledged. The work at the Advanced Light Source at Lawrence Berkeley National Laboratory was supported by US Department of Energy (Contract DE-AC03-76SF00098). References and Notes (1) Heidelberger, C.; Chaudhuri, N. K.; Danneberg, P.; Mooren, D.; Griesbach, L.; Duschinsky, R.; Schnitzer, R. J.; Pleven, E.; Scheiner, J. Nature 1957, 179, 663-666. (2) Singh, U. P.; Ghose, R.; Ghose, A. K. Inorg. Chim. AsBioinor. 1987, 136, 21-24. (3) Singh, U. P. Cryst. Res. Technol. 1989, 24, K145-K147. (4) Braun, E.; Eichen, Y.; Sivan, U.; Ben-Yoseph, G. Nature 1998, 391, 775-778. (5) de Pablo, P. J.; Moreno-Herrero, F.; Colchero, J.; Herrero, J. G.; Herrero, P.; Baro, A. M.; Ordejon, P.; Soler, J. M.; Artacho, E. Phys. ReV. Lett. 2000, 85, 4992-4995. (6) Storm, A. J.; van Noort, J.; de Vries, S.; Dekker, C. Appl. Phys. Lett. 2001, 79, 3881-3883. (7) Tran, P.; Alavi, B.; Gruner, G. Phys. ReV. Lett. 2000, 85, 15641567. (8) Porath, D.; Bezryadin, A.; de Vries, S.; Dekker, C. Nature 2000, 403, 635-638. (9) Yoo, K. H.; Ha, D. H.; Lee, J. O.; Park, J. W.; Kim, J.; Kim, J. J.; Lee, H. Y.; Kawai, T.; Choi, H. Y. Phys. ReV. Lett. 2001, 87, 198102. (10) Rakitin, A.; Aich, P.; Papadopoulos, C.; Kobzar, Y.; Vedeneev, A.; Lee, J.; Xu, J. Phys. ReV. Lett. 2001, 86, 3670-3673. (11) Fink, H.; Schonenberger, C. Nature 1999, 398, 407-410. (12) Kasumov, A.; Kociak, M.; Gueron, S.; Reulet, B.; Volkov, V.; Klinov, D.; Bouchiat, H. Science 2001, 291, 280-282.

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