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Dissociative electron attachment in uracil: Total anion yield
Chemical Physics Letters 408 (2005) 426–428 www.elsevier.com/locate/cplett
Dissociative electron attachment in uracil: Total anion yield K. Aflatooni 1, A.M. Scheer, P.D. Burrow
*
Department of Physics and Astronomy, University of Nebraska-Lincoln, Lincoln, NE 68588-0111, United States Received 11 March 2005; in final form 21 April 2005 Available online 17 May 2005
Abstract The total relative yield of anions produced by electron impact on uracil has been measured at energies below ionization. Peaks associated with vibrational Feshbach, shape and core-excited resonances are observed, although the relative sizes differ from those measured using mass analysis. Observation of positive ionization in uracil permits normalization to the ionization cross section. Feil et al. [J. Phys. B: At. Mol. Opt. Phys. 37 (2004) 3013] have used the semi-classical Deutsch–Ma¨rk ionization cross section for this purpose. Using the D–M cross section for normalization, we find that the cross section for production of (U–H) is substantially smaller than their mass selected result. 2005 Elsevier B.V. All rights reserved.
1. Introduction Bond breaking induced by low energy electron impact on bio-molecules is well known to take place through the dissociative electron attachment (DEA) process. Double- and single-strand breaks have been observed [1] in DNA at electron energies at which coreexcited temporary anion states are formed. Single-strand breaks have been measured more recently [2] at energies below 4 eV where shape resonances of the DNA bases are known to occur [3]. However, in most key compounds such as the DNA and RNA bases and amino acids, absolute cross sections for production of mass selected anion fragments in the gas phase are rare, and the estimates that have been put forth are unconfirmed. Such measurements in compounds with low vapor pressures are hindered by a host of experimental challenges. In this Letter, we report the electron energy dependence of the total relative yield of anion fragments in the RNA base uracil, the subject of a number of recent *
Corresponding author. Fax: +1 402 472 2879. E-mail address: [email protected] (P.D. Burrow). 1 Permanent address: Department of Physics, Fort Hays State University, Hays, KS 67601-4099, United States. 0009-2614/$ - see front matter 2005 Elsevier B.V. All rights reserved. doi:10.1016/j.cplett.2005.04.085
papers [4–7]. In addition, we have also observed the yield of positive ions from threshold to the maximum in the cross section. Although there are no experimental determinations of the absolute ionization cross section to which our data could be normalized, Feil et al. [7] have recently used the calculated semi-classical Deutsch–Ma¨rk (D–M) ionization cross section [8] for such a purpose. With this normalization, we derive approximate cross sections for the total DEA yield. Our result for the production of (U–H) , however, differs significantly from the cross section of Feil et al. [7].
2. Experimental Our apparatus consists of the electron transmission spectrometer used in earlier studies of the temporary negative ion states of the DNA bases [3] and halosubstituted uracils [6], but modified to allow collection of anion current inside the hot collision cell. A static collision cell is employed which is attached to a sample oven containing uracil powder. Each chamber is independently temperature controlled, with the collision cell generally held approximately 10 warmer than the sample oven. As in the normal transmission apparatus, a
K. Aflatooni et al. / Chemical Physics Letters 408 (2005) 426–428
magnetically collimated trochoidal monochromator [9] is used to provide the energy selected electron beam. The spectrometer was modified to include guard electrodes on each end of the anion collecting cylinder to allow measurement of small currents with a vibrating reed electrometer. Because of its short length, the geometry of the cell is not optimum for our purposes, and there will be ion losses at the ends of the cell. However, since our measurements involve ratios of positive and negative ion currents, we do not believe this is a serious source of error. Efforts were made to keep the collision region as electric field-free as possible to prevent ions with thermal energies from being drawn out by field penetration at the ends of the collision cell and to eliminate the collection of trapped electrons [10].
3. Results and discussion Fig. 1 shows the anion current produced by electron impact on uracil as a function of electron energy. The energy scale is determined by positioning the pro-
Fig. 1. Total relative yield of negative ions as a function of electron energy in uracil. The vertical line marks the vertical ionization energy. The horizontal dashed line indicates the zero in the collected ion current. The ion current above 9 eV is reduced in size by a factor of 103/3.
427
nounced low energy peak at 1.01 eV, as located by Denifl et al. [5]. Below the threshold for production of negative ions, 0.6 eV, some evidence was seen for structure that appears to be artifactual and we have omitted this until further study can be made. The vertical ionization energy is indicated by a line at 9.5 eV, as determined from photoelectron spectroscopy [11]. Above this energy the total ion current is completely dominated by the production of positive ions and is shown reduced by a factor of 103/3. Because of the finite electron beam resolution (100 meV), positive ion production just below the ionization threshold also contrib0utes and obscures the negative ion yield above 8.5 eV. The detailed studies of Denifl et al. [5] using mass analysis have shown that the anion yield below 4 eV arises from a single anion species, namely (U–H) , the parent anion minus a hydrogen atom. Above 4 eV a variety of fragments are observed with peaks in the summed cross sections (T.D. Ma¨rk, private communication) near 5, 6.2, 6.9 and 9.5 eV. The dominant anion in this range appears to be OCN , but we note that the yield of H was not determined. The initial rough estimates [5] of the DEA cross sections for these products were carried out by comparison to known DEA cross sections in reference molecules such as CCl4 and SF6. The relative amounts of uracil and the calibrant gas in the molecular beam were determined by observing the response of an ion gauge to the background gas in the vacuum chamber. However, condensation of uracil on the chamber walls greatly reduces its density in the background gas relative to that of the calibrant, and consequently the cross sections were overestimated. At an energy of 1.6 eV, the yield of (U–H) was given approximately as 1.6 · 10 16 cm2. (We avoid a comparison at the sharp 1.01 eV peak because of possible resolution differences between our experiments.) The earlier cross section has been recently superceded by the work of Feil et al. [7] who gave a value of 1.6 · 10 17 cm2 at 1.6 eV. This value was obtained by observation of positive ionization in uracil and ultimate normalization to a calculated ionization cross section derived using the semi-classical Deutsch–Ma¨rk (D–M) formalism [8]. However, the experimental approach involves a number of assumptions about detection efficiencies for both positive and negative ions of the same mass and the relative efficiencies for anions of different mass and, presumably, different initial kinetic energies. For these reasons, an independent and more direct evaluation of the cross section is appropriate. To gain confidence in the operation of our apparatus in this mode, we tested it in N2O by measuring the ratio of the negative ion current at the 2.25 eV DEA peak to the total positive ion current at the maximum of the positive ionization cross section (115 eV) at fixed target density and electron beam current. The ratio of these
428
K. Aflatooni et al. / Chemical Physics Letters 408 (2005) 426–428
currents was found to be within 10% of that given by the known DEA [12] and ionization [13] cross sections. In uracil, the ratio of anion current at 1.6 eV to positive ion current at the cross section maximum was found to be 2.8 · 10 4. Taking the D–M cross section [7] to be 15.7 · 10 16 cm2, the cross section for (U–H) at 1.7 eV is thus found to be 4.4 · 10 19 cm2, approximately 36 times smaller than that given by Feil et al. The similarly reduced cross section for the sharp peak at 1.01 eV, assigned to a vibrational Feshbach resonance elsewhere [6], allows resolution of a puzzle involving our study of resonances in uracil using electron transmission spectroscopy (ETS). If the cross section had been the size initially suggested [4,5], approximately 30% of the theoretical maximum inelastic cross section, it would be difficult to understand its absence in the total scattering cross section, since such values are typical of low lying shape resonances readily observed by ETS. In the region of core-excited states above 4 eV, the maximum at 5.9 eV is similarly calibrated to be 5.5 · 10 19 cm2. This also falls well below the summed mass analyzed fragment cross sections of Feil et al., which did not include H . The shape of the peaks also differs, which may be a consequence of the omission of H . An additional cause for the discrepancies above lies in kinetic energy discrimination in the transport of ions to the mass spectrometer. Because the (U–H) anions will have near thermal energies, it is likely that the apparatus collects these anions more efficiently than it does the more energetic fragments produced at high energy. The most serious source of error in our experiment is likely due to potential fields at the ends of the collision cell that could change the fraction of thermal ions collected relative to more energetic ions. From the sensitivity of the currents to applied voltages at these electrodes, we estimate that the errors in the cross sections are less than ±50%. We have no independent way to vouch for the accuracy of the calculated D–M cross sections. Feil et al. [7] argue for an error in the 5–20% range, based on comparisons in other molecules. Determination of the total absolute cross section without reference to a computed ionization cross section remains a worthwhile goal. We note an interesting comparison between the results reported here and those of Boudaiffa et al. [14] for electron damage to DNA on a surface. These authors report an effective cross section of 3.4 · 10 15 cm2 for breaking a DNA molecule consisting of 3199 base pairs at 10 eV. This corresponds to 5 · 10 19 cm2 per base, as they point out. From their earlier data [1], the cross section at 5.9 eV appears to be roughly 4–5 times smaller than that at 10 eV, thus
yielding an effective cross section of approximately 1 · 10 19 cm2 per base at the lower energy. As we report here, the total DEA cross section of uracil, an RNA base, at this energy is 5.5 · 10 19 cm2. Given the complexities inherent in the analysis of the surface data, this comparison should not be over interpreted, however, the similarity of these values reinforces the role played by the DEA process in DNA bond breaking. Total cross section measurements in the DNA bases will be required to further pursue this line of inquiry. Finally, the gas phase cross sections given here are approximately 400 times smaller than originally estimated using the relative ion gauge readings alluded to earlier. Given that this latter method continues to be used, for example, as in a recent study of DEA in alanine [15], it seems likely that such cross sections are overestimated by more than the claimed order of magnitude.
Acknowledgments We are grateful to S. Feil and T. Ma¨rk for providing their tabulated data.
References [1] B. Boudaiffa, P. Cloutier, D. Hunting, M.A. Huels, L. Sanche, Science 287 (2000) 1658. [2] F. Martin, P.D. Burrow, Z. Cai, P. Cloutier, D. Hunting, L. Sanche, Phys. Rev. Lett. 93 (2004) 068101. [3] K. Aflatooni, G.A. Gallup, P.D. Burrow, J. Phys. Chem. A 102 (1998) 6205. [4] G. Hanel, B. Gstir, S. Denifl, P. Scheier, M. Probst, B. Farizon, M. Farizon, E. Illenberger, T.D. Ma¨rk, Phys. Rev. Lett. 90 (2003) 188104. [5] S. Denifl, S. Ptasinska, G. Hanel, B. Gstir, M. Probst, P. Scheier, T.D. Ma¨rk, J. Chem. Phys. 120 (2004) 6557. [6] A.M. Scheer, K. Aflatooni, G.A. Gallup, P.D. Burrow, Phys. Rev. Lett. 92 (2004) 068102. [7] S. Feil, K. Gluch, S. Matt-Leubner, P. Scheier, J. Limtrakul, M. Probst, H. Deutsch, K. Becker, A. Stamatovic, T.D. Ma¨rk, J. Phys. B: At. Mol. Opt. Phys. 37 (2004) 3013. [8] H. Deutsch, P. Scheier, K. Becker, T.D. Ma¨rk, Int. J. Mass Spectrom. 233 (2004) 13. [9] A. Stamatovic, G.J. Schulz, Rev. Sci. Instrum. 41 (1970) 423. [10] G.J. Schulz, Phys. Rev. 112 (1958) 150. [11] N.S. Hush, A.S. Cheung, Chem. Phys. Lett. 34 (1975) 11. [12] D. Rapp, D.D. Briglia, J. Chem. Phys. 43 (1965) 1480. [13] D. Rapp, P. Englander-Golden, J. Chem. Phys. 43 (1965) 1464. [14] B. Boudaiffa, P. Cloutier, D. Hunting, M.A. Huels, L. Sanche, Radiat. Res. 157 (2002) 227. [15] S. Ptasinska, S. Denifl, P. Candori, S. Matejcik, P. Scheier, T.D. Ma¨rk, Chem. Phys. Lett. 403 (2005) 107.
Dissociative electron attachment in uracil: Total anion yield K. Aflatooni 1, A.M. Scheer, P.D. Burrow
*
Department of Physics and Astronomy, University of Nebraska-Lincoln, Lincoln, NE 68588-0111, United States Received 11 March 2005; in final form 21 April 2005 Available online 17 May 2005
Abstract The total relative yield of anions produced by electron impact on uracil has been measured at energies below ionization. Peaks associated with vibrational Feshbach, shape and core-excited resonances are observed, although the relative sizes differ from those measured using mass analysis. Observation of positive ionization in uracil permits normalization to the ionization cross section. Feil et al. [J. Phys. B: At. Mol. Opt. Phys. 37 (2004) 3013] have used the semi-classical Deutsch–Ma¨rk ionization cross section for this purpose. Using the D–M cross section for normalization, we find that the cross section for production of (U–H) is substantially smaller than their mass selected result. 2005 Elsevier B.V. All rights reserved.
1. Introduction Bond breaking induced by low energy electron impact on bio-molecules is well known to take place through the dissociative electron attachment (DEA) process. Double- and single-strand breaks have been observed [1] in DNA at electron energies at which coreexcited temporary anion states are formed. Single-strand breaks have been measured more recently [2] at energies below 4 eV where shape resonances of the DNA bases are known to occur [3]. However, in most key compounds such as the DNA and RNA bases and amino acids, absolute cross sections for production of mass selected anion fragments in the gas phase are rare, and the estimates that have been put forth are unconfirmed. Such measurements in compounds with low vapor pressures are hindered by a host of experimental challenges. In this Letter, we report the electron energy dependence of the total relative yield of anion fragments in the RNA base uracil, the subject of a number of recent *
Corresponding author. Fax: +1 402 472 2879. E-mail address: [email protected] (P.D. Burrow). 1 Permanent address: Department of Physics, Fort Hays State University, Hays, KS 67601-4099, United States. 0009-2614/$ - see front matter 2005 Elsevier B.V. All rights reserved. doi:10.1016/j.cplett.2005.04.085
papers [4–7]. In addition, we have also observed the yield of positive ions from threshold to the maximum in the cross section. Although there are no experimental determinations of the absolute ionization cross section to which our data could be normalized, Feil et al. [7] have recently used the calculated semi-classical Deutsch–Ma¨rk (D–M) ionization cross section [8] for such a purpose. With this normalization, we derive approximate cross sections for the total DEA yield. Our result for the production of (U–H) , however, differs significantly from the cross section of Feil et al. [7].
2. Experimental Our apparatus consists of the electron transmission spectrometer used in earlier studies of the temporary negative ion states of the DNA bases [3] and halosubstituted uracils [6], but modified to allow collection of anion current inside the hot collision cell. A static collision cell is employed which is attached to a sample oven containing uracil powder. Each chamber is independently temperature controlled, with the collision cell generally held approximately 10 warmer than the sample oven. As in the normal transmission apparatus, a
K. Aflatooni et al. / Chemical Physics Letters 408 (2005) 426–428
magnetically collimated trochoidal monochromator [9] is used to provide the energy selected electron beam. The spectrometer was modified to include guard electrodes on each end of the anion collecting cylinder to allow measurement of small currents with a vibrating reed electrometer. Because of its short length, the geometry of the cell is not optimum for our purposes, and there will be ion losses at the ends of the cell. However, since our measurements involve ratios of positive and negative ion currents, we do not believe this is a serious source of error. Efforts were made to keep the collision region as electric field-free as possible to prevent ions with thermal energies from being drawn out by field penetration at the ends of the collision cell and to eliminate the collection of trapped electrons [10].
3. Results and discussion Fig. 1 shows the anion current produced by electron impact on uracil as a function of electron energy. The energy scale is determined by positioning the pro-
Fig. 1. Total relative yield of negative ions as a function of electron energy in uracil. The vertical line marks the vertical ionization energy. The horizontal dashed line indicates the zero in the collected ion current. The ion current above 9 eV is reduced in size by a factor of 103/3.
427
nounced low energy peak at 1.01 eV, as located by Denifl et al. [5]. Below the threshold for production of negative ions, 0.6 eV, some evidence was seen for structure that appears to be artifactual and we have omitted this until further study can be made. The vertical ionization energy is indicated by a line at 9.5 eV, as determined from photoelectron spectroscopy [11]. Above this energy the total ion current is completely dominated by the production of positive ions and is shown reduced by a factor of 103/3. Because of the finite electron beam resolution (100 meV), positive ion production just below the ionization threshold also contrib0utes and obscures the negative ion yield above 8.5 eV. The detailed studies of Denifl et al. [5] using mass analysis have shown that the anion yield below 4 eV arises from a single anion species, namely (U–H) , the parent anion minus a hydrogen atom. Above 4 eV a variety of fragments are observed with peaks in the summed cross sections (T.D. Ma¨rk, private communication) near 5, 6.2, 6.9 and 9.5 eV. The dominant anion in this range appears to be OCN , but we note that the yield of H was not determined. The initial rough estimates [5] of the DEA cross sections for these products were carried out by comparison to known DEA cross sections in reference molecules such as CCl4 and SF6. The relative amounts of uracil and the calibrant gas in the molecular beam were determined by observing the response of an ion gauge to the background gas in the vacuum chamber. However, condensation of uracil on the chamber walls greatly reduces its density in the background gas relative to that of the calibrant, and consequently the cross sections were overestimated. At an energy of 1.6 eV, the yield of (U–H) was given approximately as 1.6 · 10 16 cm2. (We avoid a comparison at the sharp 1.01 eV peak because of possible resolution differences between our experiments.) The earlier cross section has been recently superceded by the work of Feil et al. [7] who gave a value of 1.6 · 10 17 cm2 at 1.6 eV. This value was obtained by observation of positive ionization in uracil and ultimate normalization to a calculated ionization cross section derived using the semi-classical Deutsch–Ma¨rk (D–M) formalism [8]. However, the experimental approach involves a number of assumptions about detection efficiencies for both positive and negative ions of the same mass and the relative efficiencies for anions of different mass and, presumably, different initial kinetic energies. For these reasons, an independent and more direct evaluation of the cross section is appropriate. To gain confidence in the operation of our apparatus in this mode, we tested it in N2O by measuring the ratio of the negative ion current at the 2.25 eV DEA peak to the total positive ion current at the maximum of the positive ionization cross section (115 eV) at fixed target density and electron beam current. The ratio of these
428
K. Aflatooni et al. / Chemical Physics Letters 408 (2005) 426–428
currents was found to be within 10% of that given by the known DEA [12] and ionization [13] cross sections. In uracil, the ratio of anion current at 1.6 eV to positive ion current at the cross section maximum was found to be 2.8 · 10 4. Taking the D–M cross section [7] to be 15.7 · 10 16 cm2, the cross section for (U–H) at 1.7 eV is thus found to be 4.4 · 10 19 cm2, approximately 36 times smaller than that given by Feil et al. The similarly reduced cross section for the sharp peak at 1.01 eV, assigned to a vibrational Feshbach resonance elsewhere [6], allows resolution of a puzzle involving our study of resonances in uracil using electron transmission spectroscopy (ETS). If the cross section had been the size initially suggested [4,5], approximately 30% of the theoretical maximum inelastic cross section, it would be difficult to understand its absence in the total scattering cross section, since such values are typical of low lying shape resonances readily observed by ETS. In the region of core-excited states above 4 eV, the maximum at 5.9 eV is similarly calibrated to be 5.5 · 10 19 cm2. This also falls well below the summed mass analyzed fragment cross sections of Feil et al., which did not include H . The shape of the peaks also differs, which may be a consequence of the omission of H . An additional cause for the discrepancies above lies in kinetic energy discrimination in the transport of ions to the mass spectrometer. Because the (U–H) anions will have near thermal energies, it is likely that the apparatus collects these anions more efficiently than it does the more energetic fragments produced at high energy. The most serious source of error in our experiment is likely due to potential fields at the ends of the collision cell that could change the fraction of thermal ions collected relative to more energetic ions. From the sensitivity of the currents to applied voltages at these electrodes, we estimate that the errors in the cross sections are less than ±50%. We have no independent way to vouch for the accuracy of the calculated D–M cross sections. Feil et al. [7] argue for an error in the 5–20% range, based on comparisons in other molecules. Determination of the total absolute cross section without reference to a computed ionization cross section remains a worthwhile goal. We note an interesting comparison between the results reported here and those of Boudaiffa et al. [14] for electron damage to DNA on a surface. These authors report an effective cross section of 3.4 · 10 15 cm2 for breaking a DNA molecule consisting of 3199 base pairs at 10 eV. This corresponds to 5 · 10 19 cm2 per base, as they point out. From their earlier data [1], the cross section at 5.9 eV appears to be roughly 4–5 times smaller than that at 10 eV, thus
yielding an effective cross section of approximately 1 · 10 19 cm2 per base at the lower energy. As we report here, the total DEA cross section of uracil, an RNA base, at this energy is 5.5 · 10 19 cm2. Given the complexities inherent in the analysis of the surface data, this comparison should not be over interpreted, however, the similarity of these values reinforces the role played by the DEA process in DNA bond breaking. Total cross section measurements in the DNA bases will be required to further pursue this line of inquiry. Finally, the gas phase cross sections given here are approximately 400 times smaller than originally estimated using the relative ion gauge readings alluded to earlier. Given that this latter method continues to be used, for example, as in a recent study of DEA in alanine [15], it seems likely that such cross sections are overestimated by more than the claimed order of magnitude.
Acknowledgments We are grateful to S. Feil and T. Ma¨rk for providing their tabulated data.
References [1] B. Boudaiffa, P. Cloutier, D. Hunting, M.A. Huels, L. Sanche, Science 287 (2000) 1658. [2] F. Martin, P.D. Burrow, Z. Cai, P. Cloutier, D. Hunting, L. Sanche, Phys. Rev. Lett. 93 (2004) 068101. [3] K. Aflatooni, G.A. Gallup, P.D. Burrow, J. Phys. Chem. A 102 (1998) 6205. [4] G. Hanel, B. Gstir, S. Denifl, P. Scheier, M. Probst, B. Farizon, M. Farizon, E. Illenberger, T.D. Ma¨rk, Phys. Rev. Lett. 90 (2003) 188104. [5] S. Denifl, S. Ptasinska, G. Hanel, B. Gstir, M. Probst, P. Scheier, T.D. Ma¨rk, J. Chem. Phys. 120 (2004) 6557. [6] A.M. Scheer, K. Aflatooni, G.A. Gallup, P.D. Burrow, Phys. Rev. Lett. 92 (2004) 068102. [7] S. Feil, K. Gluch, S. Matt-Leubner, P. Scheier, J. Limtrakul, M. Probst, H. Deutsch, K. Becker, A. Stamatovic, T.D. Ma¨rk, J. Phys. B: At. Mol. Opt. Phys. 37 (2004) 3013. [8] H. Deutsch, P. Scheier, K. Becker, T.D. Ma¨rk, Int. J. Mass Spectrom. 233 (2004) 13. [9] A. Stamatovic, G.J. Schulz, Rev. Sci. Instrum. 41 (1970) 423. [10] G.J. Schulz, Phys. Rev. 112 (1958) 150. [11] N.S. Hush, A.S. Cheung, Chem. Phys. Lett. 34 (1975) 11. [12] D. Rapp, D.D. Briglia, J. Chem. Phys. 43 (1965) 1480. [13] D. Rapp, P. Englander-Golden, J. Chem. Phys. 43 (1965) 1464. [14] B. Boudaiffa, P. Cloutier, D. Hunting, M.A. Huels, L. Sanche, Radiat. Res. 157 (2002) 227. [15] S. Ptasinska, S. Denifl, P. Candori, S. Matejcik, P. Scheier, T.D. Ma¨rk, Chem. Phys. Lett. 403 (2005) 107.