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Absolute partial and total electron ionization cross sections of uracil
Accepted Manuscript Title: Absolute Partial and Total Electron Ionization Cross sections of Uracil Author: M.A. Rahman E. Krishnakumar PII: DOI: Reference:
S1387-3806(15)00342-5 http://dx.doi.org/doi:10.1016/j.ijms.2015.10.003 MASPEC 15519
To appear in:
International Journal of Mass Spectrometry
Received date: Revised date: Accepted date:
16-7-2015 3-10-2015 5-10-2015
Please cite this article as: M.A. Rahman, E. Krishnakumar, Absolute Partial and Total Electron Ionization Cross sections of Uracil, International Journal of Mass Spectrometry (2015), http://dx.doi.org/10.1016/j.ijms.2015.10.003 This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain.
Absolute Partial and Total Electron Ionization Cross sections of Uracil M. A. Rahman and E. Krishnakumar Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai 400 005, India Abstract
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Absolute partial and total electron ionization cross sections for uracil in the gas phase as a function of energy up to 500 eV are measured using the well-known Relative Flow Technique (RFT). These
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measurements have significant consequences for the study of radiation damage, tests of several theoretical models and application of the RFT for molecules existing in solid form at room
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temperature. Also presented are the thresholds for the formation of various fragment ions from uracil and the comparison of total ionization cross section with the existing results.
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Keywords: Electron ionization, Uracil, Partial cross sections, Total cross sections
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1. Introduction
The study of biomolecules (DNA bases and complex aromatic organic molecules) in isolated conditions is of fundamental interest for modelling their behavior in biological systems. Moreover, the
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discovery of complex organic molecules, amino acids and nucleobases of extra-terrestrial origin in
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many meteorites and astrophysical environments [1] over the last few decades have also generated a lot of interest in the study of these molecules.
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A number of studies on the interaction of radiation (charge particles) with isolated nucleic acid bases have been carried out [2 – 11] for understanding the radiation damage in biological systems. The interaction of high energy radiation with the biological media produces large number of secondary electrons through a cascading process of ionization. These electrons being the most abundant charged particles play the dominant role in converting the kinetic energy into chemical energy causing DNA damage. It has been demonstrated that electrons at energies well below ionization thresholds can induce substantial yields of single- and double-strand breaks in DNA by dissociative electron attachment process [12]. Ionization in the biological medium becomes important at higher energies. The Monte Carlo track simulations for radiation damage studies [13] always accounts for ionization. However, the probability of simultaneous ionization and dissociation (known as dissociative ionization) has not been considered in these simulations, due to lack of data. In a biochemical model, it is not only necessary to know the initial energy deposition and probability of damage, but also the chemical identity of the damage products to predict subsequent steps of the damage process. Detailed data for biochemical modeling includes electron collision crosssections (partial and total) for nucleobases. A complete set of measured data on the absolute partial
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and total ionization cross sections of these molecules have not yet been reported. Feil et al. [7] reported total ionization cross sections up to 200 eV for uracil by normalizing their values at 100 eV with theoretical data [7]. Absolute total ion cross sections and partial cross sections for a few dominant ions for the DNA and RNA bases up to 200 eV have been reported recently [8 – 11]. However, for uracil, these results [8] are considerably lower than the available theoretical results and
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lower than that obtained by Feil et al. [7] by as much as 60 %. Burgt et al. [2] have measured and summed ion yield curves for all fragments and normalized them with the calculated total cross sections to obtain total ionization cross sections for Uracil. On the theoretical side, Bernhardt and
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Paretzke [14] calculated total ionization cross sections for all the nucleobases using semi-classical Deutsch-Märk formalism [15] as well as Binary-Encounter Bethe (BEB) formalism [16]. Mozejko
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and Sanche also reported total ionization cross sections for all nucleobases using BEB formalism [17]. Recently, Vinodkumar et al. [18] have reported total ionization calculations for DNA and RNA bases
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using Spherical Complex Optical Potential (SCOP) model and scattering theory. Considering the paucity of data and its importance, we have measured absolute partial and total electron ion cross sections for uracil up to 500 eV.
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For measurement of absolute cross sections using crossed beams, accurate determination of target density and electron current in the interaction volume are needed. It is difficult to determine the density profile in a target beam and its exact volume overlap with the electron beam. This difficulty is
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greatly overcome by normalization using the Relative Flow Technique (RFT). The basic principle of RFT is to compare the intensity of the species of interest with that of a standard species of known
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cross section [19]. For accurate application of RFT, one has to be careful to ensure that the measurements for both the gases are carried out under identical experimental conditions (identical
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interaction volume). This is achieved by allowing the gas to flow through a capillary or an array of capillaries under molecular flow conditions. The molecules effusing out of it will have a specific angular distribution independent of the nature of the gas and the pressure (in the range where molecular flow condition holds). The effusive molecular beam profile and hence the geometry of the interaction volume will be independent of the nature of the gas. The only change will be a constant multiplier which depends on the pressure behind the capillary, which can be measured accurately. Most of the large organic molecules and bio-molecules exist in solid phase at room
temperature and have very low vapour pressure. To study electron collision on these molecules, they must be heated in order to increase their vapour pressure. Measuring the pressure behind the capillary at such elevated temperatures is technically a very difficult task due to the absence of appropriate manometers. However, recent data [20 - 23] on vapor pressure of DNA and RNA bases around sublimation temperatures allows accurate estimation of the pressure behind the capillary as a function of temperature. In order to use the RFT for molecules which are in solid state at room temperature, we designed a special oven and made suitable arrangements in the experimental setup so that both the standard gas and the sample gas can pass through the same capillary to fulfill the RFT conditions.
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While the pressure behind the capillary of the standard gas can be measured using a capacitance manometer suitably coupled outside the main vacuum chamber, the pressure behind the capillary for the solid samples are determined from the temperature.
2. Apparatus and Measurement procedure
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The experimental setup for measurement of absolute electron ionization cross sections has been described in detail elsewhere [24]. The schematic of this is given in Fig 1. It consists of a magnetically collimated and pulsed electron gun, an effusive molecular beam formed by a capillary, a
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Time of Flight Mass Spectrometer (ToFMS) to mass select the ions, a pair of micro-channel plates of 50 mm diameter in chevron configuration as detector, a Faraday cup to measure the incident electron
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current and the associated electronics to store the ion signal as a function of the mass and electron energy. The ionizing electron energy scan and multichannel data storage were controlled by a
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computer for measurements using a software code developed in-house. The signal from the MCP as a function of the incident electron energy, was recorded using a Fast CompTec Model 7887 multipleevent time digitizer with 250 ps time-resolution, which is also used as an ultra fast Multiscaler/TOF
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system and time-resolved single ion counting.
Fig. 1: (Color online) Schematic diagram of the experimental arrangement. The ToF set up on the right hand side was used for the present measurements. The short ToF setup on the left hand side is a velocity map imaging spectrometer, which is not used in the present measurements.
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Energy resolution of the electron beam was about 0.7 eV (FWHM). Time averaged electron beam current in the Faraday cup was chosen to be around 50 pA during measurements. Note that the accuracy of determination of the appearance energies for ionic fragments depends strongly on the primary electron energy scale calibration. Argon atoms were chosen as reference objects, and the
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energy scale was calibrated using the ion yield curve of Ar+ from Ar at the ionization threshold.
Fig. 2: (Color online) Schematic of the oven used to heat the sample.
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The target beam is generated by heating the powder sample in the oven and allowing the
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sublimated molecules to effuse through a capillary of radius 0.2 mm and length of 10 mm directly into the collision region. The oven, as shown in Figure 2 can be used to heat the sample to a temperature
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of 400O C. The temperature is measured using an E-type thermocouple attached to the oven. Temperature control and monitoring unit is also designed to set and monitor the required temperature with a reading accuracy of better than 0.1O C. Uniform heating of the sample across the container and the capillary was assured by measuring the temperature at both ends of the capillary using a similar thermocouple after filling the sample in the container. The temperature dependence of vapor pressure of Uracil has been reported by Bardi et al..
[21] for the temperature range of 452 – 587 K, De Barros et al.. [22] for 320 – 440 K and Brutteni et al.. [23] for 384 - 494 K. These measurements have been shown to be fairly consistent with each other. Brutteni et al.. have provided the temperature dependence of vapour pressure in a convenient form, which we have used for determining the vapour pressure of Uracil. It is given as
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For normalization of cross sections using the RFT, a standard gas (Argon) has to be flown through the same capillary. To accomplish this, the back side of the oven is attached to a gas line from outside (Fig. 2) and the pressure in this line is measured by a capacitance manometer. For the RFT, we measure the intensities, Nu, of an ion u of the sample gas under study and Ns of an ion of known ionization cross section σu can be related with known cross sections (σs), as
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cross sections which is used as a secondary standard (s), under identical conditions. The partial
where, N represents the intensity of each ion, F is the flow rate of individual gases, M the molecular weight of each gas and I, the time averaged electron beam current. This equation can be further
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simplified since F.M1/2 is proportional to pressure P behind the capillary under molecular flow conditions as,
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The samples were obtained from Sigma–Aldrich in the form of crystalline powder with a
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minimum purity of 99% and used without any further purification. The measurements were carried
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out after gradually heating the Uracil sample up to 435 K in the oven for about a couple of days to completely pump out the water present in the sample powder, as this temperature is well below their
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decomposition temperature of about 300o C [25]. One of the difficulties in these measurements is preventing thermal decomposition of the molecules. We studied the possibility of thermal decomposition by measuring the mass spectra at fixed electron energy as a function of temperature over the range of temperature that we used. No change in the relative intensity of the mass spectra or no new fragments were observed with change in temperature. The possible thermal decomposition of the sample could also be identified by the change of color of the powder on visual inspection of the remaining sample after the experiment. By taking all these into account, we ensured that thermal decomposition did not contribute any erroneous signal in our measurements. The measurement procedure consisted of the following steps. First, the mass spectrum was measured in the crossed beam mode at ionizing electron energy of 100 eV and temperature of 435 K. Then the ion yield curves for all the fragments were measured simultaneously. Next, standard gas Argon is introduced through the same capillary and ion counts for Ar+ were recorded at the same temperature and energy. The Argon gas was also flown at different temperatures and counts were recorded to see the effect of change of temperature on Argon counts. We found that the Ar ion counts were independent of the temperature in the range we investigated. During the crossed beam
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measurements, there is a contribution from the background molecules that fill the vacuum chamber uniformly due to scattering at the surfaces. This contribution needs to be subtracted from the measured crossed beam data in order to have the contribution from the beam alone. For this, a separate set of measurements is carried out by placing the oven in such a way that no molecular beam is available in the interaction region. The background mass spectrum obtained in this configuration each mass fragment. The mass scale was calibrated using Ar+ and Ar++.
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was subtracted and normalized to the electron current and pressure to obtain the normalized counts for In order to ensure complete collection and detection of the ions, we had to use biases on the
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ToF spectrometer which did not provide the best mass resolution. This resulted in several mass peaks overlapping with each other in certain mass ranges. For getting the individual contributions for ions of
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a given mass to charge ratio (m/e), each of the envelopes was deconvoluted to individual peaks assuming Gaussian shape of uniform half width. The area under each Gaussian was taken as the
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contribution due to that particular ion. The sum of the individual peaks obtained was further
3.
Uncertainties and their estimation
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normalized to the total area under the particular envelope.
There are uncertainties in both the relative as well as the absolute cross sections that we
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measured. The uncertainties in the relative cross sections arise from possible overlap volume change in the electron and molecular beams as we change the electron energy. In addition to this, the relative
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intensities of each of the peaks in the mass spectrum have uncertainty due to the Gaussian deconvolutions that we employed. The contribution due to this varies depending on the overall shape
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of the envelopes of peaks and the statistics. In addition to this, while making the absolute cross section measurements additional uncertainties enter from the measurement of electron current, pressure and statistical errors from ion counting. The entire electron energy was scanned within a time of 300 s which ensured that the experimental conditions did not change significantly during one complete scan. The reproducibility of these ion yield curves was within 1 % over the entire energy range. In order to limit nonlinear effects due to pulse pile up, the maximum total count rate (inclusive of all the masses) was kept at the most one-tenth of the electron beam pulse rate, though we have used a multihit card for data acquisition. We found that the error due to the non-linearity of the ion detection system was practically zero. During measurements the temperature is measured at the far-end of the oven. It was assured that the temperature remains same at the other end of the oven and at both end of capillary within 0.1o C, which causes an uncertainty of less than 0.1 % in the vapor pressure.
The
uncertainty quoted in [23] in the temperature dependence of the vapour pressure data is close to 4.0 %. For normalization of the uracil cross sections to absolute values, we have used the Ar single ionization cross section from [26] which quotes an uncertainty of 5%. We have used this data since it is the most recent absolute measurement and is consistent with other measurements [26 - 28]. A
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compilation of the data on Ar single ionization cross section from these gives a standard deviation of 2.9 %. Assuming 5% uncertainty in the Ar data and combining it with the uncertainty in the counting statistics including that arising from the Gaussian deconvolution of the peaks, pressure measurements and the uncertainty in the ion yield curve provides a total uncertainty of 6.5 % in the present measurements in absolute cross sections for all the ions which are at least 10% of the intensity of the
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parent ion. Similar uncertainty holds for ions below m/e = 20 as they were very well resolved. For
Results and discussion
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ions of m/e > 20 and of intensity less than 10 % of the parent ion, the uncertainty is as much as 10%.
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Fig. 3: Uracil molecular structure
Fig. 4: (Color online) Relative intensities of various ions from Uracil at 100 eV electron energy.
The relative intensities of various ions from Uracil at 100 eV electron energy are given in Fig. 4. There are several reports on the electron impact mass spectra of uracil [3 - 5, 29 - 30], including the most recent one by Denifl et al.. [6]. In Table 1 relative intensities of four principal fragments HNCH+/CO+ (m/e = 28), OCN+ (m/e = 42), C3H3NO+ (m/e = 69) and Uracil parent ion (m/e = 112),
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from various measurements are compared. As can be seen from the table, there appears to be considerable differences in the relative intensities in various measurements. It is difficult to identify the reason for this, but could be either one or a combination of both of two types of systematic errors that may affect the observed relative ion intensity distribution in the mass spectra. The first one is the variation in efficiency of the detector as a function of the mass to charge ratio. The second one is the
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collection and transmission efficiency of the mass spectrometer. The collection and transmission depends on initial kinetic energy and angular distribution of the ions. In addition, their mass to charge ratio may also come into effect when a quadrupole mass spectrometer is used for mass analysis. The
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lighter ions are likely to be affected more by the kinetic energy discrimination, while the heavier ions are likely to be affected by the detection efficiencies. In the present measurements, we have ensured
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that the uncertainties due to collection and detection efficiencies are minimised by using a large pulsed field extraction, a ToF mass spectrometer, a large area detector and appropriate detector biases
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and sensitive pulse counting electronics.
Table 1: Comparison of relative ion intensities with the earlier measurements
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At 200 eV Denifl et Present Coupier et al. [6] al. [5] 41 60 94 100
64 68 55 100
94 102 85 100
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28 42 69 112
Relative Intensity of prominent Ions fragments At 70 eV Present NIST Ulrich et Smith et Rice et [3] al. [29] al. [30] al. [4] 62 27 30 100 64 45 60 38 125 55 55 35 30 80 100 100 100 100 100
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m/e (amu)
Jochims et al. [31] have used photoionization mass spectrometry with synchrotron radiation
in the 6–22 eV photon energy range to investigate fragmentation pathways, ionization energies and ion appearance energies (AE) and compared them with the results of electron impact. The fragmentation pattern and the dynamics that leads to it have also been studied by Zhou et al. [32] using pump-probe laser photoionization technique in combination with detailed ab initio calculations. The fragmentation pattern that we observe with the major cation fragments as C3H3NO+ (m/e = 69), OCN+(m/e = 42), HNCH+/CO+ (m/e = 28), as well as a parent cation U+ are consistent with these reports. The observation of the fragments with m/z ratios of 40–43 amu and 69 amu have been attributed to the dissociation of uracil through the extrusion of the HCNO and the complementary C3H3NO+ fragment [32] as:
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It may undergo further dissociation for the production of other ion fragments. It has also been shown [31] that the initial loss of HNCO always involves C-2 and N-3 as shown in Figure 3, and leads to the most stable intermediates [M – OCNH]+, which can undergo the subsequent fragmentations. This sequential scheme achieves simultaneous breaking of the N3−C4 and N1−C2 bonds through retro Diels–Alder reaction leading to the loss of the HNCO group as pointed out in [31].
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The prominent peak at m/z = 42, which has been assigned to OCN+ can be produced only through hydrogen transfer by tautomerization as discussed by Zhou et al.. [32].
Another
fragmentation pathway with m/z = 69 as precursor ion leads, by rupture of the central carbon–carbon
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bond, to the formation of HCNH+ (m/z = 28),
The m/z = 28 ion is very intense and can be assigned to the astrophysically important fragment
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HCNH+ species as has been pointed out earlier [31]. The possible pathway to form m/e = 28 involves breaking the bonds N3−C2 and C4−C5, producing HCNH+ and CHCONHCO. As compared to the = 28 has been assigned to HCNH+ [32].
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product of CO+, the energy of the final products involving HCNH+ is much lower and hence the m/z Bond cleavage along N3–C4 and C5–C6 can yield fragments C2H2+ (26 amu) and C2H3+ (27 amu) from uracil. The 27 amu peak has two possible assignments as C2H3+ and HCN+, where the
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latter to be more probable as discussed in [32] from the thermodynamic energy estimations and the
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stability of HCN. It is worth mentioning that the complementary neutral fragment in the direct fragmentation of the parent cation into the HCN+ is C3H3N. This dissociation channel may be related
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to that producing the C3H3N+ cation and the neutral HCN, which requires charge shift between the dissociation products. The peaks between 12 - 14 amu are assignable to hydrocarbon fragments, C+, CH+ and CH2+ or N+ respectively.
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Fig. 5: (Color online) Ion yield curves near the threshold region for the formation of various cations from neutral uracil by electron impact. Filled squares are the measured data and the solid lines are their linear fits. We measured the ion yield curves for the energy range of 0 – 500 eV for all prominent ions. Some of these curves near the threshold energies are given in Figure 5. The changes in slope of the
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ion yield curves are indicated by solid lines superimposed on them in order to obtain the appearance energies (AE). The solid lines were obtained using linear fit. In Table 2, the AEs of all major ions investigated are listed. The present AE values in this table were derived by reading out the
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intersection of linear fit with the energy axis. The uncertainties quoted here include the reading error
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and the systematic error in measurement of AE.
Appearance Energy (eV)
Ion Fragment
e- impact [6]
Photon
Impact
[31]
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Present measurements
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m/e
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Table 2: Appearance energies for various fragment ions from Uracil.
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12
C+ +
12±0.9
30±0.9
-
-
11±0.9
26.5±0.9
-
-
CH
14
N+/ CH2+
12.5±0.7
21±0.7
-
-
15
CH3+/NH+
13.5±0.7
19.5±0.7
-
-
16
O+/NH2+
12.0±0.7
-
-
-
25
+
C2H
14.0±0.7
32.5±0.9
-
-
26
C2H2+/CN+
15.5±0.7
19.0±0.7
-
27
+
HCN
13.5±0.7
18±0.9
14.77±0.92
28
HCNH+ /CO+
13.7±0.7
--
13.83±0.39
12.0±0.7
22.7±0.7
-
40
20.0±0.9
14.5±0.9
18.5±0.9
+
11.5±0.7
14.5±0.7
C2H2N C2H3N +
13.75±0.05
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14.0±0.9
+
C3H3/C2NH
-
-
14.06±0.1
13.32±0.18
12.95±0.05
15.5±0.7
13.41±0.10
13.25±0.05
43
OCNH
13.5±0.6
-
13.36±0.30
13.6±0.2
53
C3H3N+
14.5±0.7
19±0.7
-
-
56
C2H4N2+
12.5±0.7
19.0±0.7
13.20±0.25
-
68
C3H2NO+
11.5±0.9
14.0±0.7
12.75±0.66
13.4±0.05
69
+
C3H3NO
11.5±0.7
13.2±0.7
10.89±0.07
10.95±0.05
112
C4H4N2O2+
9.5±0.7
9.59 ± 0.08
9.15 ± 0.03
OCN
--
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42
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13.0±0.7 +
M
41
+
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39
C3H2/ C2N
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38
+
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Table 2 also includes the AE measured by Denifl et al. [6] by electron impact and Jochim et
al. [31] using photon impact on Uracil molecule. In most cases we observed 2 appearance energies due to a clear change in the slope of ion yield curve near threshold. Two slopes could be due to the particular ion being formed by two different pathways, with the second one contributing at higher energies. This kind of change of slope in ion yield curve is not apparent in parent ion and HCNH+ fragment ion (Fig. 5). The parent ion, which is the most abundant ion, has a single AE value of 9.5 ± 0.7 eV. This and the first thresholds for other ions are more or less consistent with the results of Denifl et al. within the measurement uncertainties.
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Fig. 6a: (color online) Absolute partial ionization cross sections for various ions from Uracil. (Upper panel: filled squares – C3HNO+ (67 amu), filled circles – C2H4N2+ (56 amu) and filled triangles – C2H+
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(25 amu). Lower panel: filled squares – CO+/HCNH+ (28 amu), filled circles – C3H3NO+ (69 amu) and filled triangles – C3H2NO+ (68 amu).)
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Fig. 6b: (color online) Absolute partial ionization cross sections for various ions from Uracil. (Upper
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panel: filled squares – C+ (12 amu), filled circles – CH+ (13 amu) and filled triangles – CH2+/N+ (14
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amu), empty squares – NH+ (15 amu) and empty circles – O+/NH2+ (16 amu). Lower panel: filled squares – C2H2+ (26 amu), filled circles – HCN+ (27 amu), filled triangles – C3H2+ (38 amu), empty
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squares – C3H3N+ (53 amu).)
Partial cross sections for all the dominant ions are shown in Fig. 6a, 6b, and 6c. The partial cross sections for a selected set of ions are also given in Table 3. The cross sections for most of the ions rise quite steeply towards their respective peak values and then decrease rather slowly toward higher energies. However, we note that the electron energy at which the cross sections reach the maximum show a pattern as a function of the mass. This is shown in Fig. 7, where we have plotted the peak energy as a function of m/e of the ions. For ions up to m/e = 40 the cross sections appear to peak by 80 eV. For the rest of the ions, leaving aside m/e = 12, 15 and 16 the cross sections peak at about 100 eV. For m/e = 15, which is most probably NH+ and m/e = 16, most of which is likely to be O+, the cross sections peak at about 150 eV, while that for C+ (m/e = 12) the cross section peaks at an energy little over 160 eV. The peak position is determined by availability of states in the ionization continuum, which increases with electron energy. The shift of the peaks from 80 eV to higher values shows that the lighter ions have more available channels of formation as compared to the heavier ones. One way this happens is through the opening of multiple ionization channels of heavier ions
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which fragments giving rise to lighter ions. The increase in the peak position for low mass ions as compared to the heavier ones, as shown in Fig 7, can thus be understood as due to contribution from multiple ionization of the molecule. Thus one can say that for the lighter ions (m/e < 40), multiple
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ionization is a major contributing factor above 80 eV or so.
Figure 6c: (color online) Absolute partial ionization cross sections for various ions from Uracil. (Upper panel: filled squares – OCN+ (42 amu), filled circles – C2H2N+ (40 amu) and filled triangles – C2NH+ (39 amu). Lower panel: filled squares – U+ (112 amu), filled circles – CHN2+ (41 amu) and filled triangles – OCNH+ (43 amu).)
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Fig. 7: Electron energy corresponding to the peak cross section for ions as a function of their mass to charge ratio.
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Table 3: Partial ionization cross sections for prominent ions and total ionization cross section for
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Uracil molecule.
Partial Ionization Cross Sections for prominent ions (x 10-18 cm2)
Electron
Cross
C4H4N2O2+
C3H3NO+
C3H2NO+
OCNH+
OCN+
CN2H+
C2H2N+
CO+/
m/e = 112
m/e=69
m/e=68
m/e=43
m/e=42
m/e=41
m/e=40
HCNH+
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(eV)
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Energy
Total ion
m/e=28
Section (10-16 cm2)
1.75
0
0
0
0
0
0
0
0.03
10.3
0.13
0
0
0
0.12
0
0
0.16
26.1
1.41
0.13
0
0
1.01
0.19
0
0.36
50.7
5.55
0.51
0
0.11
2.15
0.15
0.06
0.72
72.0
8.87
0.78
0.42
0.85
4.45
0.21
0.12
1.03
100
14.6
1.31
0.78
1.38
5.41
0.16
0.23
1.45
16
136
24.6
2.39
1.28
4.75
8.71
0.31
0.62
2.07
17
170
36.2
3.76
2.71
11.1
11.9
0.77
1.77
2.76
18
199
48.2
5.51
4.41
19.8
16.6
1.19
3.49
3.47
19
220
59.8
8.25
6.81
32.5
20.5
1.83
6.58
4.17
20
236
69.1
10.5
8.90
47.2
25.2
3.19
10.6
4.83
25
280
99.1
26.3
23.2
126
55.8
25.1
40.8
8.08
10 11 12 13 14 15
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298
109
37.5
36.1
178
79.2
62.5
70.4
10.6
35
318
118
43.8
48.4
210
102
101
94.7
12.9
40
337
127
49.0
61.6
242
122
130
115
14.9
45
352
131
53.3
71.7
263
137
145
128
16.3
50
351
132
53.5
77.6
276
145
150
134
17.0
55
355
134
54.3
83.9
287
155
152
146
17.7
60
358
137
56.2
88.5
300
161
159
162
18.5
65
363
140
57.4
93.1
309
168
163
171
19.1
70
365
141
58.1
93.1
316
168
164
178
19.5
75
358
142
58.6
95.1
319
171
165
184
19.7
80
364
142
59.1
97.2
321
165
166
196
20.0
85
363
141
58.2
96.7
322
165
162
195
19.9
90
359
141
58.4
96.2
321
163
160
204
20.0
95
358
138
57.7
95.3
100
351
134
55.9
94.2
125
350
134
56.9
93.4
150
332
127
56.5
175
318
121
56.1
200
318
122
55.4
225
301
115
54.1
250
290
111
275
285
109
300
279
107
260
375 400 425 450 475 500
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us
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350
158
94.1
287
151
141
184
18.3
91.1
276
145
136
170
17.5
89.1
266
140
131
165
17.1
86.7
255
134
126
157
16.4
51.2
80.8
252
132
124
143
15.7
49.8
76.1
238
124
117
133
15.0
48.1
73.9
232
121
114
125
14.6
99.2
47.0
72.4
226
118
111
120
13.9
256
97.9
46.9
71.0
218
113
107
112
13.5
249
95.2
46.4
69.3
211
110
104
112
13.2
239
91.3
45.6
66.6
208
108
103
101
12.7
233
89.1
43.2
64.4
194
101
95.8
97.8
12.2
223
85.1
43.3
62.5
192
99.4
94.6
97.5
11.9
217
83.0
42.2
61.1
188
97.0
92.5
90.3
11.5
214
81.7
41.3
58.7
182
93.9
89.7
84.6
11.2
318
164
200
19.7
310
164
152
206
19.4
302
159
149
195
19.1
M
d
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325
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30
Page 16 of 23
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Fig. 8: (color online) Absolute total ionization cross section for Uracil. (filled stars - present measurements normalized to theory,
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measurements; filled circles - Shafranyosh et al. [8]; empty stars – Feil et al. [7] relative empty squares - Feil et al..
[7] calculations, circles -
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Vinodkumar et al.. [18], triangles - Mozejko et al.. [17].)
The measured total ion cross sections obtained by summing all the partial cross sections are given in Table 3. These are also shown in Fig. 8. The available experimental and theoretical values
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are also shown in the figure. Of the two experimental data, the one by Feil et al.. [7] was obtained by normalization to the calculated cross section based on the semi-classical Deutsch–M¨ark formalism at
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100 eV (16 x 10-16 cm2). Shafranyosh et al. [8] used a crossed beam method and measured the absolute cross sections directly by measuring the total ion current, the target beam density by
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collecting and weighing the mass of the target beam condensed on a collector and the volume overlap between the beams using the geometrical details of the set up. The results of Feil et al. [7] are more or less consistent with theoretical calculations in terms of the relative shape as well. All the theoretical calculations appear to agree with each other. The cross sections obtained by Shafranyosh et al. [8] appear to rise much faster at low energies as compared to the calculations and peak at 95 eV to a value of 10 x 10 -16 cm2. The cross sections then appear to decrease relatively slowly towards 200 eV. The most notable aspect of this data is the considerably lower peak value of 10 x 10-16 cm2. The present measurements agree with the results of Feil et al. and the theoretical calculations in terms of the relative shape to a great extent. All these cross section curves exhibit the typical shape with a maximum at energy very close to 80 eV and a steady decline towards higher energies. The significant difference in present measurements with the previous results is the relatively large peak value. The peak cross section obtained by Feil et al.. is smaller by 20 % of our measured value of 20 x 10 -16 cm2. This difference is larger for the results by Vinodkumar et al.. [18] and Mozejko et al.. [17] who obtained a peak cross section of 15.1 x 10 -16 cm2 14.6 x 10 -16 cm2, respectively. The most striking is that the value obtained by us is twice that obtained by Shafranyosh et al. [8]. It is difficult to
Page 17 of 23
understand the source of this disparity. One possible reason may be due to overestimation of the overlap volume between the electron beam and the molecular beam by Shafranyosh et al. [8]. We note that the shape of the total ion crosssections obtained by us is rising relatively slowly as compared to the other data, including theoretical results. Below about 40 eV, the cross sections obtained by Feil et al. [7] and Shafranyosh et al. [8] are larger than what we have measured. The reasons for these
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differences are unclear as of now. The theoretical results also appear to overestimate the cross sections at lower energies. We have noticed similar overestimations in the case of NF3 [24] as well.
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5. Conclusion
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We have studied dissociative ionization of Uracil by electron impact up to 500 eV. From the recorded mass spectra as a function of electron energy we obtain the yield curves for all fragment ions along
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with that of the parent ion. The various fragments have been identified and their appearance energies have been measured. Using the relative flow technique, we have normalized the ion yield curves to the respective absolute partial ionization cross sections. The partial cross sections have been summed
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up to obtain the total ion cross section and it is compared with the available experimental and theoretical results. The absolute total ionization cross sections of the DNA biomolecules and biomolecule precursors are most frequently estimated by applying binary-encounter-Bethe and semi-
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classical Deutsch-M¨ark formalisms and our measurement in this energy range will be a bench-mark to test these models. It will have immediate application in Particle Track simulations where the data
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for dissociative ionization (partial ionization cross section) for all fragments of DNA bases in this energy range is not available and the total absolute cross section is used from the theoretical
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calculations.
References:
1. M. P. Callahan, K. E. Smith, H. James Cleaves, J. Ruzicka, J. C. Stern, D. P. Glavin, C. H. House and J. P. Dworkin, Carbonaceous meteorites contain a wide range of extraterrestrial nucleobases, PNAS 108 (2011)13995.
2. Peter J.M. van der Burgt, F. Mahon, G. Barrett and M. L. Gradziel, Electron impact fragmentation of thymine: partial ionization, cross sections for positive Fragments, Eur. Phys. J. D 68 (2014) 151 3. NIST database (mass spectrum) : NIST Mass Spectrometry Data Center, 1998 http://webbook.nist.gov/cgi/cbook.cgi?Name=uracil&Units=SI&cMS=on#Refs
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4. J.M. Rice, G.O. Dudek and M. Barber, Mass Spectra of Nucleic Acid Derivatives: Pyrimidines, J. Am. Chem. Soc. 87 (1965) 4569. 5. B. Coupier, B. Farizon, M. Farizon, M.J. Gaillard, F. Gobert, N.V. de Castro Faria, G. Jalbert, S. Ouaskit, M. Carre´, B. Gstir, G. Hanel, S. Denifl, L. Feketeova, P. Scheier and T. D. Ma¨rk, Inelastic interactions of protons and electrons with biologically relevant
ip t
molecules, Eur. Phys. J. D 20 (2002) 459.
6. S. Denifl, B. Sonnweber, G. Hanel, P. Scheier and T.D. M¨ark, Threshold electron impact
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ionization studies of uracil, IJMS 238 (2004) 47.
7. S. Feil, K. Gluch, S. Matt-Leubner, P. Scheier, J. Limtrakul, M. Probst, H. Deutsch, K.
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Becker, A. Stamatovic and T. D. M¨ark, Partial cross sections for positive and negative ion formation following electron impact on uracil, J. Phys. B: At. Mol. Opt. Phys. 37
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(2004) 3013.
8. I. I. Shafranyosh and M. I. Sukhoviya, Inelastic collisions of the uracil molecules with electrons, J. Chem. Phys. 137 (2012)184303.
Baryshnikov and V. A.
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9. B. F. Minaev, M. I. Shafranyosh, Y. Y. Svida, M. I. Sukhoviya, I. I. Shafranyosh, G. V. Minaeva, Fragmentation of the adenine and guanine molecules
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induced by electron collisions, J. Chem. Phys. 140 (2014) 175101. 10. I. I. Shafranyosh, M. I. Sukhoviya and M. I. Shafranyosh, Absolute cross sections of positive(2006) 4155.
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and negative-ion production in electron collision with cytosine molecules, J. Phys. B. 39
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11. I. I. Shafranyosh, M. I. Sukhoviya, M. I. Shafranyosh and L. L. Shimon, Formation of Positive and Negative Ions of Thymine Molecules under the Action of Slow Electrons, Technical Physics 53 (2008) 1538.
12. B. Boudaõffa, P. Cloutier, D. Hunting, M. A. Huels and L. Sanche, Resonant Formation of DNA Strand Breaks by Low-Energy (3 to 20 eV) Electrons, Science 287 (2000) 1658.
13. H. Nikjoo, P. O’Neill, M. Terrissol and D. T. Goodhead, Quantitative modelling of DNA damage using Monte Carlo track structure method, Radiat. Environ. Biophys. 38(1999) 31.
14. Ph. Bernhardt and H.G. Paretzke, Calculation of electron impact ionization cross sections of DNA using the Deutsch–Märk and Binary–Encounter–Bethe formalisms, IJMS 223 ( 2003) 599. 15. H. Deutsch, K. Becker, S. Matt and T.D. Mark, Theoretical determination of absolute electron-impact ionization cross sections of molecules, IJMS 197 (2000) 37.
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16. Y. K. Kim and M. E. Rudd, Binary-encounter-dipole model for electron-impact ionization, Phy. Rev. A 50 (1994)3954. 17. P. Moz˙ejko and L. Sanche, Cross section calculations for electron scattering from DNA and RNA bases, Radiat. Environ. Biophys. 42 (2003) 201.
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18. M. Vinodkumar, C. Limbachiya, M. Barot, M. Swadia and A. Barot., Electron impact total ionization cross sections for all the components of DNA and RNA molecule, IJMS 339 (2013) 16.
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20. C. J. Colyer, Ph. D. thesis, University of Adelaide (2011).
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19. E. Krishnakumar and S.K. Srivastava, J. Phys. B: At. Mol. and Opt. Phys. 21 (1988) 1055.
21. G. Bardi, L. Bencivenni, D. Ferro, B. Martini, S. Nunziantecesaro and R. Teghil, Thermodynamic study of the vaporization of uracil, Thermochim. Acta. 40 (1980) 275.
an
22. A. L. F. de Barros, A. Medina, F. Zappa, J.M. Pereira, E. Bessa, M.H.P. Martins, L.F.S. Coelho, W. Wolff and N.V. de Castro Faria, Nucl. Instr. Methods in Phys. Res. A 560 (2006)
23. B. Brunetti, V.
Piacente and G.
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219.
Portalone, Sublimation Enthalpies of Some Methyl
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Derivatives of Uracil from Vapor Pressure Measurements, J. Chem. Eng. Data (2000)
te
24. M. A. Rahman, S. Gangopadhyay, C. Limbachiya, K. N. Joshipura and E. Krishnakumar, Electron ionization of NF3, IJMS 319 – 320 (2012) 48.
Ac ce p
25. M. A. Huels, I. Hahndorf, E. Illenberger and L. Sanche, Resonant dissociation of DNA bases by subionization electrons, J. Chem. Phys. 108 (1998) 1309.
26. R. Rejoub, B. G. Lindsay and R. F. Stebbings, Determination of the absolute partial and total cross sections for electron-impact ionization of the rare gases, Phys. Rev. A, 65 (2002) 042713.
27. H. C. Straub, P. Renault, B. G. Lindsay, K. A. Smith and R. F. Stebbings, Absolute partial and total cross sections for electron-impact ionization of argon from threshold to 1000 eV, Phys. Rev. A, 52 (1995) 1115. 28. Ce Ma, C. R. Sporleder and R. A. Bonham, A pulsed electron beam time of flight apparatus for measuring absolute electron impact ionization and dissociative ionization cross sections, Rev. Sci. Instr. 62 (1991) 909.
29. J. Ulrich, R. Teoule, R. Massot and A. Cornu, Etude de la fragmentation de dérivés de l'uracile et de la thymine par spectrométrie de masse, Org. Mass Spectrom. 2 (1969) 1183.
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30. K. C. Smith and R.T. Aplin, A Mixed Photoproduct of Uracil and Cysteine ( 5-S-Cysteine-6hydrouracil ) : A Possible Model for the in Vivo Cross-Linking of Deoxyribonucleic Acid and Protein by Ultraviolet Light, Biochemistry 5 (1966) 2125. 31. H. W. Jochims , M. Schwell , H. Baumga¨rtel and S. Leach, Photo-ion mass spectrometry and uracil in the 6–22 eV photon energy range, Chem. Phys. 314
(2005) 263.
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of adenine, thymine
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te
d
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an
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Uracil Radical Cation, J. Phys. Chem. A 116 (2012) 9217.
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32. C. Zhou, S. Matsika, M. Kotur and T. C. Weinacht, Fragmentation Pathways in the
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Highlights Detailed measurements of absolute electron ionization cross sections for Uracil.
•
Appearance potentials for various fragment ions are measured and compared.
•
A bench-mark to test the theoretical models for the ionization cross sections.
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RFT is used for molecules in solid form at room temperature for the first time.
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It has immediate application in DNA Particle Track simulation packages.
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*Graphical Abstract (for review)
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S1387-3806(15)00342-5 http://dx.doi.org/doi:10.1016/j.ijms.2015.10.003 MASPEC 15519
To appear in:
International Journal of Mass Spectrometry
Received date: Revised date: Accepted date:
16-7-2015 3-10-2015 5-10-2015
Please cite this article as: M.A. Rahman, E. Krishnakumar, Absolute Partial and Total Electron Ionization Cross sections of Uracil, International Journal of Mass Spectrometry (2015), http://dx.doi.org/10.1016/j.ijms.2015.10.003 This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain.
Absolute Partial and Total Electron Ionization Cross sections of Uracil M. A. Rahman and E. Krishnakumar Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai 400 005, India Abstract
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Absolute partial and total electron ionization cross sections for uracil in the gas phase as a function of energy up to 500 eV are measured using the well-known Relative Flow Technique (RFT). These
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measurements have significant consequences for the study of radiation damage, tests of several theoretical models and application of the RFT for molecules existing in solid form at room
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temperature. Also presented are the thresholds for the formation of various fragment ions from uracil and the comparison of total ionization cross section with the existing results.
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Keywords: Electron ionization, Uracil, Partial cross sections, Total cross sections
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1. Introduction
The study of biomolecules (DNA bases and complex aromatic organic molecules) in isolated conditions is of fundamental interest for modelling their behavior in biological systems. Moreover, the
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discovery of complex organic molecules, amino acids and nucleobases of extra-terrestrial origin in
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many meteorites and astrophysical environments [1] over the last few decades have also generated a lot of interest in the study of these molecules.
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A number of studies on the interaction of radiation (charge particles) with isolated nucleic acid bases have been carried out [2 – 11] for understanding the radiation damage in biological systems. The interaction of high energy radiation with the biological media produces large number of secondary electrons through a cascading process of ionization. These electrons being the most abundant charged particles play the dominant role in converting the kinetic energy into chemical energy causing DNA damage. It has been demonstrated that electrons at energies well below ionization thresholds can induce substantial yields of single- and double-strand breaks in DNA by dissociative electron attachment process [12]. Ionization in the biological medium becomes important at higher energies. The Monte Carlo track simulations for radiation damage studies [13] always accounts for ionization. However, the probability of simultaneous ionization and dissociation (known as dissociative ionization) has not been considered in these simulations, due to lack of data. In a biochemical model, it is not only necessary to know the initial energy deposition and probability of damage, but also the chemical identity of the damage products to predict subsequent steps of the damage process. Detailed data for biochemical modeling includes electron collision crosssections (partial and total) for nucleobases. A complete set of measured data on the absolute partial
Page 1 of 23
and total ionization cross sections of these molecules have not yet been reported. Feil et al. [7] reported total ionization cross sections up to 200 eV for uracil by normalizing their values at 100 eV with theoretical data [7]. Absolute total ion cross sections and partial cross sections for a few dominant ions for the DNA and RNA bases up to 200 eV have been reported recently [8 – 11]. However, for uracil, these results [8] are considerably lower than the available theoretical results and
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lower than that obtained by Feil et al. [7] by as much as 60 %. Burgt et al. [2] have measured and summed ion yield curves for all fragments and normalized them with the calculated total cross sections to obtain total ionization cross sections for Uracil. On the theoretical side, Bernhardt and
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Paretzke [14] calculated total ionization cross sections for all the nucleobases using semi-classical Deutsch-Märk formalism [15] as well as Binary-Encounter Bethe (BEB) formalism [16]. Mozejko
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and Sanche also reported total ionization cross sections for all nucleobases using BEB formalism [17]. Recently, Vinodkumar et al. [18] have reported total ionization calculations for DNA and RNA bases
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using Spherical Complex Optical Potential (SCOP) model and scattering theory. Considering the paucity of data and its importance, we have measured absolute partial and total electron ion cross sections for uracil up to 500 eV.
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For measurement of absolute cross sections using crossed beams, accurate determination of target density and electron current in the interaction volume are needed. It is difficult to determine the density profile in a target beam and its exact volume overlap with the electron beam. This difficulty is
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greatly overcome by normalization using the Relative Flow Technique (RFT). The basic principle of RFT is to compare the intensity of the species of interest with that of a standard species of known
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cross section [19]. For accurate application of RFT, one has to be careful to ensure that the measurements for both the gases are carried out under identical experimental conditions (identical
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interaction volume). This is achieved by allowing the gas to flow through a capillary or an array of capillaries under molecular flow conditions. The molecules effusing out of it will have a specific angular distribution independent of the nature of the gas and the pressure (in the range where molecular flow condition holds). The effusive molecular beam profile and hence the geometry of the interaction volume will be independent of the nature of the gas. The only change will be a constant multiplier which depends on the pressure behind the capillary, which can be measured accurately. Most of the large organic molecules and bio-molecules exist in solid phase at room
temperature and have very low vapour pressure. To study electron collision on these molecules, they must be heated in order to increase their vapour pressure. Measuring the pressure behind the capillary at such elevated temperatures is technically a very difficult task due to the absence of appropriate manometers. However, recent data [20 - 23] on vapor pressure of DNA and RNA bases around sublimation temperatures allows accurate estimation of the pressure behind the capillary as a function of temperature. In order to use the RFT for molecules which are in solid state at room temperature, we designed a special oven and made suitable arrangements in the experimental setup so that both the standard gas and the sample gas can pass through the same capillary to fulfill the RFT conditions.
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While the pressure behind the capillary of the standard gas can be measured using a capacitance manometer suitably coupled outside the main vacuum chamber, the pressure behind the capillary for the solid samples are determined from the temperature.
2. Apparatus and Measurement procedure
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The experimental setup for measurement of absolute electron ionization cross sections has been described in detail elsewhere [24]. The schematic of this is given in Fig 1. It consists of a magnetically collimated and pulsed electron gun, an effusive molecular beam formed by a capillary, a
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Time of Flight Mass Spectrometer (ToFMS) to mass select the ions, a pair of micro-channel plates of 50 mm diameter in chevron configuration as detector, a Faraday cup to measure the incident electron
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current and the associated electronics to store the ion signal as a function of the mass and electron energy. The ionizing electron energy scan and multichannel data storage were controlled by a
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computer for measurements using a software code developed in-house. The signal from the MCP as a function of the incident electron energy, was recorded using a Fast CompTec Model 7887 multipleevent time digitizer with 250 ps time-resolution, which is also used as an ultra fast Multiscaler/TOF
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system and time-resolved single ion counting.
Fig. 1: (Color online) Schematic diagram of the experimental arrangement. The ToF set up on the right hand side was used for the present measurements. The short ToF setup on the left hand side is a velocity map imaging spectrometer, which is not used in the present measurements.
Page 3 of 23
Energy resolution of the electron beam was about 0.7 eV (FWHM). Time averaged electron beam current in the Faraday cup was chosen to be around 50 pA during measurements. Note that the accuracy of determination of the appearance energies for ionic fragments depends strongly on the primary electron energy scale calibration. Argon atoms were chosen as reference objects, and the
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energy scale was calibrated using the ion yield curve of Ar+ from Ar at the ionization threshold.
Fig. 2: (Color online) Schematic of the oven used to heat the sample.
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The target beam is generated by heating the powder sample in the oven and allowing the
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sublimated molecules to effuse through a capillary of radius 0.2 mm and length of 10 mm directly into the collision region. The oven, as shown in Figure 2 can be used to heat the sample to a temperature
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of 400O C. The temperature is measured using an E-type thermocouple attached to the oven. Temperature control and monitoring unit is also designed to set and monitor the required temperature with a reading accuracy of better than 0.1O C. Uniform heating of the sample across the container and the capillary was assured by measuring the temperature at both ends of the capillary using a similar thermocouple after filling the sample in the container. The temperature dependence of vapor pressure of Uracil has been reported by Bardi et al..
[21] for the temperature range of 452 – 587 K, De Barros et al.. [22] for 320 – 440 K and Brutteni et al.. [23] for 384 - 494 K. These measurements have been shown to be fairly consistent with each other. Brutteni et al.. have provided the temperature dependence of vapour pressure in a convenient form, which we have used for determining the vapour pressure of Uracil. It is given as
Page 4 of 23
For normalization of cross sections using the RFT, a standard gas (Argon) has to be flown through the same capillary. To accomplish this, the back side of the oven is attached to a gas line from outside (Fig. 2) and the pressure in this line is measured by a capacitance manometer. For the RFT, we measure the intensities, Nu, of an ion u of the sample gas under study and Ns of an ion of known ionization cross section σu can be related with known cross sections (σs), as
us
cr
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cross sections which is used as a secondary standard (s), under identical conditions. The partial
where, N represents the intensity of each ion, F is the flow rate of individual gases, M the molecular weight of each gas and I, the time averaged electron beam current. This equation can be further
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simplified since F.M1/2 is proportional to pressure P behind the capillary under molecular flow conditions as,
M
The samples were obtained from Sigma–Aldrich in the form of crystalline powder with a
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minimum purity of 99% and used without any further purification. The measurements were carried
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out after gradually heating the Uracil sample up to 435 K in the oven for about a couple of days to completely pump out the water present in the sample powder, as this temperature is well below their
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decomposition temperature of about 300o C [25]. One of the difficulties in these measurements is preventing thermal decomposition of the molecules. We studied the possibility of thermal decomposition by measuring the mass spectra at fixed electron energy as a function of temperature over the range of temperature that we used. No change in the relative intensity of the mass spectra or no new fragments were observed with change in temperature. The possible thermal decomposition of the sample could also be identified by the change of color of the powder on visual inspection of the remaining sample after the experiment. By taking all these into account, we ensured that thermal decomposition did not contribute any erroneous signal in our measurements. The measurement procedure consisted of the following steps. First, the mass spectrum was measured in the crossed beam mode at ionizing electron energy of 100 eV and temperature of 435 K. Then the ion yield curves for all the fragments were measured simultaneously. Next, standard gas Argon is introduced through the same capillary and ion counts for Ar+ were recorded at the same temperature and energy. The Argon gas was also flown at different temperatures and counts were recorded to see the effect of change of temperature on Argon counts. We found that the Ar ion counts were independent of the temperature in the range we investigated. During the crossed beam
Page 5 of 23
measurements, there is a contribution from the background molecules that fill the vacuum chamber uniformly due to scattering at the surfaces. This contribution needs to be subtracted from the measured crossed beam data in order to have the contribution from the beam alone. For this, a separate set of measurements is carried out by placing the oven in such a way that no molecular beam is available in the interaction region. The background mass spectrum obtained in this configuration each mass fragment. The mass scale was calibrated using Ar+ and Ar++.
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was subtracted and normalized to the electron current and pressure to obtain the normalized counts for In order to ensure complete collection and detection of the ions, we had to use biases on the
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ToF spectrometer which did not provide the best mass resolution. This resulted in several mass peaks overlapping with each other in certain mass ranges. For getting the individual contributions for ions of
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a given mass to charge ratio (m/e), each of the envelopes was deconvoluted to individual peaks assuming Gaussian shape of uniform half width. The area under each Gaussian was taken as the
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contribution due to that particular ion. The sum of the individual peaks obtained was further
3.
Uncertainties and their estimation
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normalized to the total area under the particular envelope.
There are uncertainties in both the relative as well as the absolute cross sections that we
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measured. The uncertainties in the relative cross sections arise from possible overlap volume change in the electron and molecular beams as we change the electron energy. In addition to this, the relative
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intensities of each of the peaks in the mass spectrum have uncertainty due to the Gaussian deconvolutions that we employed. The contribution due to this varies depending on the overall shape
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of the envelopes of peaks and the statistics. In addition to this, while making the absolute cross section measurements additional uncertainties enter from the measurement of electron current, pressure and statistical errors from ion counting. The entire electron energy was scanned within a time of 300 s which ensured that the experimental conditions did not change significantly during one complete scan. The reproducibility of these ion yield curves was within 1 % over the entire energy range. In order to limit nonlinear effects due to pulse pile up, the maximum total count rate (inclusive of all the masses) was kept at the most one-tenth of the electron beam pulse rate, though we have used a multihit card for data acquisition. We found that the error due to the non-linearity of the ion detection system was practically zero. During measurements the temperature is measured at the far-end of the oven. It was assured that the temperature remains same at the other end of the oven and at both end of capillary within 0.1o C, which causes an uncertainty of less than 0.1 % in the vapor pressure.
The
uncertainty quoted in [23] in the temperature dependence of the vapour pressure data is close to 4.0 %. For normalization of the uracil cross sections to absolute values, we have used the Ar single ionization cross section from [26] which quotes an uncertainty of 5%. We have used this data since it is the most recent absolute measurement and is consistent with other measurements [26 - 28]. A
Page 6 of 23
compilation of the data on Ar single ionization cross section from these gives a standard deviation of 2.9 %. Assuming 5% uncertainty in the Ar data and combining it with the uncertainty in the counting statistics including that arising from the Gaussian deconvolution of the peaks, pressure measurements and the uncertainty in the ion yield curve provides a total uncertainty of 6.5 % in the present measurements in absolute cross sections for all the ions which are at least 10% of the intensity of the
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parent ion. Similar uncertainty holds for ions below m/e = 20 as they were very well resolved. For
Results and discussion
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4.
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ions of m/e > 20 and of intensity less than 10 % of the parent ion, the uncertainty is as much as 10%.
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Fig. 3: Uracil molecular structure
Fig. 4: (Color online) Relative intensities of various ions from Uracil at 100 eV electron energy.
The relative intensities of various ions from Uracil at 100 eV electron energy are given in Fig. 4. There are several reports on the electron impact mass spectra of uracil [3 - 5, 29 - 30], including the most recent one by Denifl et al.. [6]. In Table 1 relative intensities of four principal fragments HNCH+/CO+ (m/e = 28), OCN+ (m/e = 42), C3H3NO+ (m/e = 69) and Uracil parent ion (m/e = 112),
Page 7 of 23
from various measurements are compared. As can be seen from the table, there appears to be considerable differences in the relative intensities in various measurements. It is difficult to identify the reason for this, but could be either one or a combination of both of two types of systematic errors that may affect the observed relative ion intensity distribution in the mass spectra. The first one is the variation in efficiency of the detector as a function of the mass to charge ratio. The second one is the
ip t
collection and transmission efficiency of the mass spectrometer. The collection and transmission depends on initial kinetic energy and angular distribution of the ions. In addition, their mass to charge ratio may also come into effect when a quadrupole mass spectrometer is used for mass analysis. The
cr
lighter ions are likely to be affected more by the kinetic energy discrimination, while the heavier ions are likely to be affected by the detection efficiencies. In the present measurements, we have ensured
us
that the uncertainties due to collection and detection efficiencies are minimised by using a large pulsed field extraction, a ToF mass spectrometer, a large area detector and appropriate detector biases
an
and sensitive pulse counting electronics.
Table 1: Comparison of relative ion intensities with the earlier measurements
M
te
At 200 eV Denifl et Present Coupier et al. [6] al. [5] 41 60 94 100
64 68 55 100
94 102 85 100
Ac ce p
28 42 69 112
Relative Intensity of prominent Ions fragments At 70 eV Present NIST Ulrich et Smith et Rice et [3] al. [29] al. [30] al. [4] 62 27 30 100 64 45 60 38 125 55 55 35 30 80 100 100 100 100 100
d
m/e (amu)
Jochims et al. [31] have used photoionization mass spectrometry with synchrotron radiation
in the 6–22 eV photon energy range to investigate fragmentation pathways, ionization energies and ion appearance energies (AE) and compared them with the results of electron impact. The fragmentation pattern and the dynamics that leads to it have also been studied by Zhou et al. [32] using pump-probe laser photoionization technique in combination with detailed ab initio calculations. The fragmentation pattern that we observe with the major cation fragments as C3H3NO+ (m/e = 69), OCN+(m/e = 42), HNCH+/CO+ (m/e = 28), as well as a parent cation U+ are consistent with these reports. The observation of the fragments with m/z ratios of 40–43 amu and 69 amu have been attributed to the dissociation of uracil through the extrusion of the HCNO and the complementary C3H3NO+ fragment [32] as:
Page 8 of 23
It may undergo further dissociation for the production of other ion fragments. It has also been shown [31] that the initial loss of HNCO always involves C-2 and N-3 as shown in Figure 3, and leads to the most stable intermediates [M – OCNH]+, which can undergo the subsequent fragmentations. This sequential scheme achieves simultaneous breaking of the N3−C4 and N1−C2 bonds through retro Diels–Alder reaction leading to the loss of the HNCO group as pointed out in [31].
ip t
The prominent peak at m/z = 42, which has been assigned to OCN+ can be produced only through hydrogen transfer by tautomerization as discussed by Zhou et al.. [32].
Another
fragmentation pathway with m/z = 69 as precursor ion leads, by rupture of the central carbon–carbon
us
cr
bond, to the formation of HCNH+ (m/z = 28),
The m/z = 28 ion is very intense and can be assigned to the astrophysically important fragment
an
HCNH+ species as has been pointed out earlier [31]. The possible pathway to form m/e = 28 involves breaking the bonds N3−C2 and C4−C5, producing HCNH+ and CHCONHCO. As compared to the = 28 has been assigned to HCNH+ [32].
M
product of CO+, the energy of the final products involving HCNH+ is much lower and hence the m/z Bond cleavage along N3–C4 and C5–C6 can yield fragments C2H2+ (26 amu) and C2H3+ (27 amu) from uracil. The 27 amu peak has two possible assignments as C2H3+ and HCN+, where the
d
latter to be more probable as discussed in [32] from the thermodynamic energy estimations and the
te
stability of HCN. It is worth mentioning that the complementary neutral fragment in the direct fragmentation of the parent cation into the HCN+ is C3H3N. This dissociation channel may be related
Ac ce p
to that producing the C3H3N+ cation and the neutral HCN, which requires charge shift between the dissociation products. The peaks between 12 - 14 amu are assignable to hydrocarbon fragments, C+, CH+ and CH2+ or N+ respectively.
Page 9 of 23
Fig. 5: (Color online) Ion yield curves near the threshold region for the formation of various cations from neutral uracil by electron impact. Filled squares are the measured data and the solid lines are their linear fits. We measured the ion yield curves for the energy range of 0 – 500 eV for all prominent ions. Some of these curves near the threshold energies are given in Figure 5. The changes in slope of the
ip t
ion yield curves are indicated by solid lines superimposed on them in order to obtain the appearance energies (AE). The solid lines were obtained using linear fit. In Table 2, the AEs of all major ions investigated are listed. The present AE values in this table were derived by reading out the
cr
intersection of linear fit with the energy axis. The uncertainties quoted here include the reading error
us
and the systematic error in measurement of AE.
Appearance Energy (eV)
Ion Fragment
e- impact [6]
Photon
Impact
[31]
te
d
M
Present measurements
Ac ce p
m/e
an
Table 2: Appearance energies for various fragment ions from Uracil.
Page 10 of 23
12
C+ +
12±0.9
30±0.9
-
-
11±0.9
26.5±0.9
-
-
CH
14
N+/ CH2+
12.5±0.7
21±0.7
-
-
15
CH3+/NH+
13.5±0.7
19.5±0.7
-
-
16
O+/NH2+
12.0±0.7
-
-
-
25
+
C2H
14.0±0.7
32.5±0.9
-
-
26
C2H2+/CN+
15.5±0.7
19.0±0.7
-
27
+
HCN
13.5±0.7
18±0.9
14.77±0.92
28
HCNH+ /CO+
13.7±0.7
--
13.83±0.39
12.0±0.7
22.7±0.7
-
40
20.0±0.9
14.5±0.9
18.5±0.9
+
11.5±0.7
14.5±0.7
C2H2N C2H3N +
13.75±0.05
cr
14.0±0.9
+
C3H3/C2NH
-
-
14.06±0.1
13.32±0.18
12.95±0.05
15.5±0.7
13.41±0.10
13.25±0.05
43
OCNH
13.5±0.6
-
13.36±0.30
13.6±0.2
53
C3H3N+
14.5±0.7
19±0.7
-
-
56
C2H4N2+
12.5±0.7
19.0±0.7
13.20±0.25
-
68
C3H2NO+
11.5±0.9
14.0±0.7
12.75±0.66
13.4±0.05
69
+
C3H3NO
11.5±0.7
13.2±0.7
10.89±0.07
10.95±0.05
112
C4H4N2O2+
9.5±0.7
9.59 ± 0.08
9.15 ± 0.03
OCN
--
Ac ce p
te
42
d
13.0±0.7 +
M
41
+
us
39
C3H2/ C2N
-
an
38
+
ip t
13
Table 2 also includes the AE measured by Denifl et al. [6] by electron impact and Jochim et
al. [31] using photon impact on Uracil molecule. In most cases we observed 2 appearance energies due to a clear change in the slope of ion yield curve near threshold. Two slopes could be due to the particular ion being formed by two different pathways, with the second one contributing at higher energies. This kind of change of slope in ion yield curve is not apparent in parent ion and HCNH+ fragment ion (Fig. 5). The parent ion, which is the most abundant ion, has a single AE value of 9.5 ± 0.7 eV. This and the first thresholds for other ions are more or less consistent with the results of Denifl et al. within the measurement uncertainties.
Page 11 of 23
ip t cr us an M d
te
Fig. 6a: (color online) Absolute partial ionization cross sections for various ions from Uracil. (Upper panel: filled squares – C3HNO+ (67 amu), filled circles – C2H4N2+ (56 amu) and filled triangles – C2H+
Ac ce p
(25 amu). Lower panel: filled squares – CO+/HCNH+ (28 amu), filled circles – C3H3NO+ (69 amu) and filled triangles – C3H2NO+ (68 amu).)
Page 12 of 23
ip t cr us an M
Fig. 6b: (color online) Absolute partial ionization cross sections for various ions from Uracil. (Upper
d
panel: filled squares – C+ (12 amu), filled circles – CH+ (13 amu) and filled triangles – CH2+/N+ (14
te
amu), empty squares – NH+ (15 amu) and empty circles – O+/NH2+ (16 amu). Lower panel: filled squares – C2H2+ (26 amu), filled circles – HCN+ (27 amu), filled triangles – C3H2+ (38 amu), empty
Ac ce p
squares – C3H3N+ (53 amu).)
Partial cross sections for all the dominant ions are shown in Fig. 6a, 6b, and 6c. The partial cross sections for a selected set of ions are also given in Table 3. The cross sections for most of the ions rise quite steeply towards their respective peak values and then decrease rather slowly toward higher energies. However, we note that the electron energy at which the cross sections reach the maximum show a pattern as a function of the mass. This is shown in Fig. 7, where we have plotted the peak energy as a function of m/e of the ions. For ions up to m/e = 40 the cross sections appear to peak by 80 eV. For the rest of the ions, leaving aside m/e = 12, 15 and 16 the cross sections peak at about 100 eV. For m/e = 15, which is most probably NH+ and m/e = 16, most of which is likely to be O+, the cross sections peak at about 150 eV, while that for C+ (m/e = 12) the cross section peaks at an energy little over 160 eV. The peak position is determined by availability of states in the ionization continuum, which increases with electron energy. The shift of the peaks from 80 eV to higher values shows that the lighter ions have more available channels of formation as compared to the heavier ones. One way this happens is through the opening of multiple ionization channels of heavier ions
Page 13 of 23
which fragments giving rise to lighter ions. The increase in the peak position for low mass ions as compared to the heavier ones, as shown in Fig 7, can thus be understood as due to contribution from multiple ionization of the molecule. Thus one can say that for the lighter ions (m/e < 40), multiple
Ac ce p
te
d
M
an
us
cr
ip t
ionization is a major contributing factor above 80 eV or so.
Figure 6c: (color online) Absolute partial ionization cross sections for various ions from Uracil. (Upper panel: filled squares – OCN+ (42 amu), filled circles – C2H2N+ (40 amu) and filled triangles – C2NH+ (39 amu). Lower panel: filled squares – U+ (112 amu), filled circles – CHN2+ (41 amu) and filled triangles – OCNH+ (43 amu).)
Page 14 of 23
ip t cr us
an
Fig. 7: Electron energy corresponding to the peak cross section for ions as a function of their mass to charge ratio.
M
Table 3: Partial ionization cross sections for prominent ions and total ionization cross section for
d
Uracil molecule.
Partial Ionization Cross Sections for prominent ions (x 10-18 cm2)
Electron
Cross
C4H4N2O2+
C3H3NO+
C3H2NO+
OCNH+
OCN+
CN2H+
C2H2N+
CO+/
m/e = 112
m/e=69
m/e=68
m/e=43
m/e=42
m/e=41
m/e=40
HCNH+
Ac ce p
(eV)
te
Energy
Total ion
m/e=28
Section (10-16 cm2)
1.75
0
0
0
0
0
0
0
0.03
10.3
0.13
0
0
0
0.12
0
0
0.16
26.1
1.41
0.13
0
0
1.01
0.19
0
0.36
50.7
5.55
0.51
0
0.11
2.15
0.15
0.06
0.72
72.0
8.87
0.78
0.42
0.85
4.45
0.21
0.12
1.03
100
14.6
1.31
0.78
1.38
5.41
0.16
0.23
1.45
16
136
24.6
2.39
1.28
4.75
8.71
0.31
0.62
2.07
17
170
36.2
3.76
2.71
11.1
11.9
0.77
1.77
2.76
18
199
48.2
5.51
4.41
19.8
16.6
1.19
3.49
3.47
19
220
59.8
8.25
6.81
32.5
20.5
1.83
6.58
4.17
20
236
69.1
10.5
8.90
47.2
25.2
3.19
10.6
4.83
25
280
99.1
26.3
23.2
126
55.8
25.1
40.8
8.08
10 11 12 13 14 15
Page 15 of 23
298
109
37.5
36.1
178
79.2
62.5
70.4
10.6
35
318
118
43.8
48.4
210
102
101
94.7
12.9
40
337
127
49.0
61.6
242
122
130
115
14.9
45
352
131
53.3
71.7
263
137
145
128
16.3
50
351
132
53.5
77.6
276
145
150
134
17.0
55
355
134
54.3
83.9
287
155
152
146
17.7
60
358
137
56.2
88.5
300
161
159
162
18.5
65
363
140
57.4
93.1
309
168
163
171
19.1
70
365
141
58.1
93.1
316
168
164
178
19.5
75
358
142
58.6
95.1
319
171
165
184
19.7
80
364
142
59.1
97.2
321
165
166
196
20.0
85
363
141
58.2
96.7
322
165
162
195
19.9
90
359
141
58.4
96.2
321
163
160
204
20.0
95
358
138
57.7
95.3
100
351
134
55.9
94.2
125
350
134
56.9
93.4
150
332
127
56.5
175
318
121
56.1
200
318
122
55.4
225
301
115
54.1
250
290
111
275
285
109
300
279
107
260
375 400 425 450 475 500
cr
us
an
350
158
94.1
287
151
141
184
18.3
91.1
276
145
136
170
17.5
89.1
266
140
131
165
17.1
86.7
255
134
126
157
16.4
51.2
80.8
252
132
124
143
15.7
49.8
76.1
238
124
117
133
15.0
48.1
73.9
232
121
114
125
14.6
99.2
47.0
72.4
226
118
111
120
13.9
256
97.9
46.9
71.0
218
113
107
112
13.5
249
95.2
46.4
69.3
211
110
104
112
13.2
239
91.3
45.6
66.6
208
108
103
101
12.7
233
89.1
43.2
64.4
194
101
95.8
97.8
12.2
223
85.1
43.3
62.5
192
99.4
94.6
97.5
11.9
217
83.0
42.2
61.1
188
97.0
92.5
90.3
11.5
214
81.7
41.3
58.7
182
93.9
89.7
84.6
11.2
318
164
200
19.7
310
164
152
206
19.4
302
159
149
195
19.1
M
d
te
Ac ce p
325
ip t
30
Page 16 of 23
ip t cr us
Fig. 8: (color online) Absolute total ionization cross section for Uracil. (filled stars - present measurements normalized to theory,
an
measurements; filled circles - Shafranyosh et al. [8]; empty stars – Feil et al. [7] relative empty squares - Feil et al..
[7] calculations, circles -
M
Vinodkumar et al.. [18], triangles - Mozejko et al.. [17].)
The measured total ion cross sections obtained by summing all the partial cross sections are given in Table 3. These are also shown in Fig. 8. The available experimental and theoretical values
d
are also shown in the figure. Of the two experimental data, the one by Feil et al.. [7] was obtained by normalization to the calculated cross section based on the semi-classical Deutsch–M¨ark formalism at
te
100 eV (16 x 10-16 cm2). Shafranyosh et al. [8] used a crossed beam method and measured the absolute cross sections directly by measuring the total ion current, the target beam density by
Ac ce p
collecting and weighing the mass of the target beam condensed on a collector and the volume overlap between the beams using the geometrical details of the set up. The results of Feil et al. [7] are more or less consistent with theoretical calculations in terms of the relative shape as well. All the theoretical calculations appear to agree with each other. The cross sections obtained by Shafranyosh et al. [8] appear to rise much faster at low energies as compared to the calculations and peak at 95 eV to a value of 10 x 10 -16 cm2. The cross sections then appear to decrease relatively slowly towards 200 eV. The most notable aspect of this data is the considerably lower peak value of 10 x 10-16 cm2. The present measurements agree with the results of Feil et al. and the theoretical calculations in terms of the relative shape to a great extent. All these cross section curves exhibit the typical shape with a maximum at energy very close to 80 eV and a steady decline towards higher energies. The significant difference in present measurements with the previous results is the relatively large peak value. The peak cross section obtained by Feil et al.. is smaller by 20 % of our measured value of 20 x 10 -16 cm2. This difference is larger for the results by Vinodkumar et al.. [18] and Mozejko et al.. [17] who obtained a peak cross section of 15.1 x 10 -16 cm2 14.6 x 10 -16 cm2, respectively. The most striking is that the value obtained by us is twice that obtained by Shafranyosh et al. [8]. It is difficult to
Page 17 of 23
understand the source of this disparity. One possible reason may be due to overestimation of the overlap volume between the electron beam and the molecular beam by Shafranyosh et al. [8]. We note that the shape of the total ion crosssections obtained by us is rising relatively slowly as compared to the other data, including theoretical results. Below about 40 eV, the cross sections obtained by Feil et al. [7] and Shafranyosh et al. [8] are larger than what we have measured. The reasons for these
ip t
differences are unclear as of now. The theoretical results also appear to overestimate the cross sections at lower energies. We have noticed similar overestimations in the case of NF3 [24] as well.
cr
5. Conclusion
us
We have studied dissociative ionization of Uracil by electron impact up to 500 eV. From the recorded mass spectra as a function of electron energy we obtain the yield curves for all fragment ions along
an
with that of the parent ion. The various fragments have been identified and their appearance energies have been measured. Using the relative flow technique, we have normalized the ion yield curves to the respective absolute partial ionization cross sections. The partial cross sections have been summed
M
up to obtain the total ion cross section and it is compared with the available experimental and theoretical results. The absolute total ionization cross sections of the DNA biomolecules and biomolecule precursors are most frequently estimated by applying binary-encounter-Bethe and semi-
d
classical Deutsch-M¨ark formalisms and our measurement in this energy range will be a bench-mark to test these models. It will have immediate application in Particle Track simulations where the data
te
for dissociative ionization (partial ionization cross section) for all fragments of DNA bases in this energy range is not available and the total absolute cross section is used from the theoretical
Ac ce p
calculations.
References:
1. M. P. Callahan, K. E. Smith, H. James Cleaves, J. Ruzicka, J. C. Stern, D. P. Glavin, C. H. House and J. P. Dworkin, Carbonaceous meteorites contain a wide range of extraterrestrial nucleobases, PNAS 108 (2011)13995.
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4. J.M. Rice, G.O. Dudek and M. Barber, Mass Spectra of Nucleic Acid Derivatives: Pyrimidines, J. Am. Chem. Soc. 87 (1965) 4569. 5. B. Coupier, B. Farizon, M. Farizon, M.J. Gaillard, F. Gobert, N.V. de Castro Faria, G. Jalbert, S. Ouaskit, M. Carre´, B. Gstir, G. Hanel, S. Denifl, L. Feketeova, P. Scheier and T. D. Ma¨rk, Inelastic interactions of protons and electrons with biologically relevant
ip t
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cr
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Becker, A. Stamatovic and T. D. M¨ark, Partial cross sections for positive and negative ion formation following electron impact on uracil, J. Phys. B: At. Mol. Opt. Phys. 37
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Baryshnikov and V. A.
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9. B. F. Minaev, M. I. Shafranyosh, Y. Y. Svida, M. I. Sukhoviya, I. I. Shafranyosh, G. V. Minaeva, Fragmentation of the adenine and guanine molecules
d
induced by electron collisions, J. Chem. Phys. 140 (2014) 175101. 10. I. I. Shafranyosh, M. I. Sukhoviya and M. I. Shafranyosh, Absolute cross sections of positive(2006) 4155.
te
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Ac ce p
11. I. I. Shafranyosh, M. I. Sukhoviya, M. I. Shafranyosh and L. L. Shimon, Formation of Positive and Negative Ions of Thymine Molecules under the Action of Slow Electrons, Technical Physics 53 (2008) 1538.
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ip t
18. M. Vinodkumar, C. Limbachiya, M. Barot, M. Swadia and A. Barot., Electron impact total ionization cross sections for all the components of DNA and RNA molecule, IJMS 339 (2013) 16.
us
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cr
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an
22. A. L. F. de Barros, A. Medina, F. Zappa, J.M. Pereira, E. Bessa, M.H.P. Martins, L.F.S. Coelho, W. Wolff and N.V. de Castro Faria, Nucl. Instr. Methods in Phys. Res. A 560 (2006)
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Portalone, Sublimation Enthalpies of Some Methyl
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te
24. M. A. Rahman, S. Gangopadhyay, C. Limbachiya, K. N. Joshipura and E. Krishnakumar, Electron ionization of NF3, IJMS 319 – 320 (2012) 48.
Ac ce p
25. M. A. Huels, I. Hahndorf, E. Illenberger and L. Sanche, Resonant dissociation of DNA bases by subionization electrons, J. Chem. Phys. 108 (1998) 1309.
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30. K. C. Smith and R.T. Aplin, A Mixed Photoproduct of Uracil and Cysteine ( 5-S-Cysteine-6hydrouracil ) : A Possible Model for the in Vivo Cross-Linking of Deoxyribonucleic Acid and Protein by Ultraviolet Light, Biochemistry 5 (1966) 2125. 31. H. W. Jochims , M. Schwell , H. Baumga¨rtel and S. Leach, Photo-ion mass spectrometry and uracil in the 6–22 eV photon energy range, Chem. Phys. 314
(2005) 263.
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32. C. Zhou, S. Matsika, M. Kotur and T. C. Weinacht, Fragmentation Pathways in the
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Highlights Detailed measurements of absolute electron ionization cross sections for Uracil.
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Appearance potentials for various fragment ions are measured and compared.
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A bench-mark to test the theoretical models for the ionization cross sections.
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RFT is used for molecules in solid form at room temperature for the first time.
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It has immediate application in DNA Particle Track simulation packages.
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*Graphical Abstract (for review)
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