1. Justus-Liebig University, Giessen
Electron-Impact Fragmentation
and Ionisation of Uracil
Karl Kramer, Frank Scheuermann, Alexander Theiss, Roland Trassl, Paul Scheier* and Erhard Salzborn
Belfast, Monday, , 16:35 Uhr
Thank you for the nice introduction.
As you heard my name is Karl Kramer, I‘m a Diploma Student who is quite old for that, but Physics is not my first Carrier. I‘m the guy who is legally guity for modern Rebreather-Diving. I designed from scratch what nowadays is Sold als Draeger –Dolphin and Ray, and that is a Marked what feeds a lot of Engeneers and Diving-Instructors. In the Institute I‘m one of those Guys who makes or repairs the Electronics he needs, or CAD-drows what he wants to be machined and exeeds what can be build with tools that are free to be used by everybody. I improved several things on our large-scale Instrument, on both the mechanical and electronical part.
As allready said by the chairman my talk is about electron impact ionisation and fragmentation of uracil-ions.
This work has been done at the University of Giessen in the group of Professor Salzborn in collaboration with Paul Scheier from the Innsbruck University.
*:Institut für Ionenphysik, Innsbruck, Austria

2. Uracil-Ion-Electron Collisions
Motivation:
Good model for the radiation damage of living organisms on a microscopic level.
Consequential damages caused by secondary electrons.
The Measurements of collisions between electrons and Uracil-Ions are a good Modell for the radiation-damage of living organisms on a microscopic level.
When a cell is hit by some kind of radiation - either photons, ions or electrons, this may cause a primary damage but mainly leads to a shower of secondary Electrons. These electrons can further ionise and fragmentate molecules, leading to consequental damages of the cell.

3. Uracil Molecule RNA Uracil C4H4N2O2 112amu DNA Thymine C5H6N2O2 126amu
Why we had chosen Uracil? The molecular structure of Uracil is shown here. It has a mass of 112 atomic units. The biophysical relevance of Uracil is that is part of the RNA. Furthermore it has a very simliar structure as Thymine, which is part of the DNA.The diference is this H- atom is replaced by a methyl (CH3) group.
„Teimine“
25g Uracil:22€
25g Thymine: 64€

4. ESI-Setup
The Uracil is evapurated in the plasma of a Electron Cyclotron Resonance – Ion source and ions are extracted by an acceleration voltage of 10kV. The ions are focused by electrostatic lenses and separated according to their charge to mass ratio. After focusing in an electrostatic quadrupole triplett, the beam is collimated to typcally 2times2 square milimeters and enters the interaction region after a 60 degree spherical deflector. Here the beam is made to interact with an intense electron beam at an angle of 90°. The fragmentated or further ionized ions are separted by the second analyzing magnet. The reaction products are counted in a single-particle detector. whereas the primary beam current is simulaneously measured in a Faraday cup. .
* For a Product-Scan the Magentic-Field of the second analysing Magnet and the Voltage on the sperical analyser are simultaneously sweeped.
* For the absolut cross section measurements electron current, ion current and signal rate are measured simultaneously for each position of the electron gun.

5. Electron Gun
This picture shows the electron gun we are using. Electrons are emitted from a heated cathode and accelerated to maximum energies of 1000eV using a Pierce geometry.
In the interaction region we have a ribbon-shaped parallel electron beam with a length of 6 cm.
After the interaction the beam is wided up and converted to heat in a collector.
In order to measure absolute cross sections, usually the so- called formfactor needs to be determined, which describes the beam overlap. Here we avoid this by moving the whole electron beam through the ion beam. Therefore we have regions where there is no overlap between the beams and full overlap at the middle.

6. Experimental method
Using the so-called „dynamic crossed beams“ method we can get the reaction rate as shown in the picture. In the areas where is no beam overlap we measure only background, which can then be subtracted leaving the green area „S“. Using that simple forula we can get the total cross section, where Sigma is proportional to S and known factors that can directly be measured.

7. Primary-Ion Spectrum oven for small quantities
Ion current / arb. units
112
Using an oven wich was designed for small probe quantities we found ion currents close to the Uracil- peak and could not achieve suficient Uracil-ion currents. Additionally we had to refill the oven every day.
The Xenon ions were used for calibration.
typ. 22pA uracil+ with collimators at 2x2mm2

8. Low-Temperature Oven carrier with uracil 62cm
Because of the poor results of the first oven we designed a new one.
Here it is shown with the Uracil-carrier pulled out.
The oven is heated over its whole length. This allows to have a bigger reservoir
as well as sufficiently low temperatures – far away from the hot plasma.

9. Primary-Ion Spectrum low-temperature oven
112
129
132
Ion current / arb. units
With the new Oven the Uracil+ jield is significantly stronger than its Neighbours and we can now extract about 350pA instead of 22pA as before.
Setting the first analysign magnet to the mass of 112 atomic units only uracil-ions will pass through the interaction-region with the electrons.
typ. 350pA uracil+ with collimators at 2x2mm2
22pA with collimators at 1x1mm2

10. Product Spectrum e-+112Uc+->mUc+ Fragment+X 5*10-9 mbar 650 eV
not normalised count rate
This slide shows a Uracil product spectrum recorded with an Electron energy of 650 electron volt.
We can see fragments, but obvious no ionisation contributions.
As expected the complex bio-molecule is decaying into several fragment-ions upon the interaction with the high-energy electron. According to the number of the heavy atoms (C, N and O) we find several groups. Were the Groups ontaining 3 and 5 heavy components reveal the highest ion yield. Similar patterns are observed when neutral uracil interects with keV Protons (as measured by Farizon et.al.) or 100eV Electrons (as measured by Hanel et. al.).

11. Product-Spectrum Detail
5*10-9 mbar
650 eV
not normalised Countrate / arb. units
Uc+-O
Here is shown a blow up of the Uracil product spectrum, where an oyxgen atom has been removed from the Uracil.
The fragment peaks are at the expected mass to charge ratios.
The overlap of the peaks at 95 and 96 atomic mass units is a first indication that theise ions were produced in a process that releases a substantial ammount of kinetic energie (for instanc . Couldomb-Explosion of a multiply charged Precursor).

12. Fragmentation->CNO++X
This slide shows the cross section for the Fragment CNO-plus as a function of the electron energy.
The cross section has a magnitude of about 10 to minus 16 square centimeters and shows the expected energy dependance. Below 20 eV the measurement of the electron current becomes unreliable, leading to large error bars.

13. Ionisation
This slide shows the cross section for the single ionisation of Uracil- plus, which is about one order of magnitude smaller than that of the fragmentation shown before.

14. Exictation in the ion source
This Procuct spectrum was recorded without any Electron-Current and at the lowest pressure we can achieve in the interaction region.
The primary Uracil plus ions are not shown here, but apperently some fragmentation occures which can be related to exitation in the ion source. The fragment yield also varies for diffent microwave powers.
It shows that exitation is a serious problem to care about, when working with positively charged molecular ions.

15. Excitation, Detail Uc+-CO
Surprisingly we find higher CO, COH und HCHO rates when we use lower microwave powers in the ECR-ion source. For this effect we don`t have any explanation yet.

16. Residual-Gas, Detail Uc+-CO 0,25 Watt
We are also looking at the dependance of the fragments on the gas pressure in the interaction region. This shows again a product spectrum without any electron beam, for diffent gas pressures. As can be seen there is no effect on the ratios which have lost a CO, COH or HCHO -molecule.

17. Residual Gas, Detail II UC+-CNOH 0,25 Watt
This is, however, diffent for the fragmentation of a CNOH group which shows a strong dependance on the gas pressure – so it seems that some reaction channels can be related to excitation in the ion source only, whereas others are also influenced by collision with residual gas particles.

18. Conclusion
With the low-temperature oven sufficiently high ion currents for investigations of uracil became possible.
With the lowest microwave power the highest ammount of excited uracil ions was found.
Only relative measurements are possible
Fragmentation is substantially more likely than Ionisation.
Outlook: double ionisation of negative uracil ions in order to avoid metastable excited states
The conclusion so far is:
- With the low-temperature oven sufficiently high ion currents for investigations of uracil became possible.
- With the lowest microwave power the highest ammount of excited uracil ions was found.
- The shown results are preliminary measurements. Usually an ion-electron collision measurement, depending on the residual gas pressure, shows a saturation, but that could not be proved yet, due to background problems.
- Fragmentation is substantially more likely than Ionisation.
Furthermore it is planed to invetigate the double ionisation of negative uracil ions, in order to avoid metastable excited states.
Thank You for Your attension.