jra3: cold and complex (biomolecular) targets why study interaction of hci with biomolecular...
TRANSCRIPT
![Page 1: JRA3: Cold and Complex (Biomolecular) Targets Why study interaction of HCI with biomolecular targets? Basic physics: large energy transfer in a single](https://reader036.vdocuments.mx/reader036/viewer/2022062516/56649e615503460f94b5c5ee/html5/thumbnails/1.jpg)
JRA3: Cold and Complex (Biomolecular) Targets
Why study interaction of HCI with biomolecular targets?
• Basic physics: large energy transfer in a single collision!
• Applied physics: HCI as secondary products, e.g. in radiation therapy
Why “cold” targets?
• All molecules in one electronic (ground-) state
• Possibility of recoil momentum spectroscopy
Co-ordinators:
Thomas Schlathölter and Reinhard Morgenstern
![Page 2: JRA3: Cold and Complex (Biomolecular) Targets Why study interaction of HCI with biomolecular targets? Basic physics: large energy transfer in a single](https://reader036.vdocuments.mx/reader036/viewer/2022062516/56649e615503460f94b5c5ee/html5/thumbnails/2.jpg)
Tasks and Volunteers
A. Solid biomolecular targets, CEA/Caen (Huber, Lebius)
B. Ionic biomolecular targets NUI/Maynoth (O’Neill, v.d. Burgt) QUB/Belfast
(Greenwood, Williams, McCullough, OUL/London (Mason),
KVI/Groningen (Schlathölter, Morgenstern)
C. Neutral gasphase biomolecular targets CUB/ Bratislava (Matejcik), OUL/London (Mason), UIBK/Innsbruck (Scheier, Märk), LCAR/Toulouse (Moretto
Capelle)
D. Ultracold neutral targets (nanodroplets, MOT’s) UBI/Bielefeld (Stienkemeier, Werner), OUL/London (Mason), KVI/Groningen (Schlathölter, Morgenstern)
E. Datareduction and analysis UBI/Bielefeld (Werner),
![Page 3: JRA3: Cold and Complex (Biomolecular) Targets Why study interaction of HCI with biomolecular targets? Basic physics: large energy transfer in a single](https://reader036.vdocuments.mx/reader036/viewer/2022062516/56649e615503460f94b5c5ee/html5/thumbnails/3.jpg)
A. Solid biomolecular targets
In the case of a nucleic bases, a compressed powder is used as a 'solid' target, which can be bombarded with ions of different charges and energies, and at different incidence angles. Fragmentation spectra are analysed with mass-spectrometric methods.
DeOxyAdenosine
![Page 4: JRA3: Cold and Complex (Biomolecular) Targets Why study interaction of HCI with biomolecular targets? Basic physics: large energy transfer in a single](https://reader036.vdocuments.mx/reader036/viewer/2022062516/56649e615503460f94b5c5ee/html5/thumbnails/4.jpg)
0
1000
2000
3000
0 40 80 120
= 5°
*10
cou
nts
0
100
200
300
0 40 80 120
= 0°
*10
mass/charge (a.u.)
50
100
150
0 40 80 120
= 10°
O2+
(40 keV) + thymidine
inset part magnified by a factor 10
Huber et al, Caen
Dependence of the fragmentation of thymidine on the incidence angle
(m=241)
![Page 5: JRA3: Cold and Complex (Biomolecular) Targets Why study interaction of HCI with biomolecular targets? Basic physics: large energy transfer in a single](https://reader036.vdocuments.mx/reader036/viewer/2022062516/56649e615503460f94b5c5ee/html5/thumbnails/5.jpg)
B. Ionic biomolecular targets
Adaption of MALDI techniques
Desorption laser Desorption of
ions and neutrals
Laser
QUB arrangement to study neutral targets
Pulsed ion beam
![Page 6: JRA3: Cold and Complex (Biomolecular) Targets Why study interaction of HCI with biomolecular targets? Basic physics: large energy transfer in a single](https://reader036.vdocuments.mx/reader036/viewer/2022062516/56649e615503460f94b5c5ee/html5/thumbnails/6.jpg)
the principle to get an ionic target
MALDIsample
(located in a trap endcap)
laser pulse
matrixbio
molecules
3rd or 4th harmonic of our Nd:YAG-laser (355 or 266 nm)
Quantel Brilliant
pulse length: ~5 ns frequency: 50 Hz
fluence: up to 200 mJ/cm2 @ 1064 nm.
MALDI and an electrostatic trap
trapping and cooling of desorbed ions
expandingplume
(neutrals and ions)
![Page 7: JRA3: Cold and Complex (Biomolecular) Targets Why study interaction of HCI with biomolecular targets? Basic physics: large energy transfer in a single](https://reader036.vdocuments.mx/reader036/viewer/2022062516/56649e615503460f94b5c5ee/html5/thumbnails/7.jpg)
trapped ions as target for HCI/fs-laser pulses
ECRISor
fs-laser
YAG laser
trap Einzellens
MALDIsample
reflectron
detector
electrostatic analyzer
ions
TOF analysis by means of a FAST P7888 TDC (1ns resolution, 1ns deadtime, 1 GHz)
Several events per sweep: possibility of coincidence experiments
fields are switched off for MCI bunch passage!
![Page 8: JRA3: Cold and Complex (Biomolecular) Targets Why study interaction of HCI with biomolecular targets? Basic physics: large energy transfer in a single](https://reader036.vdocuments.mx/reader036/viewer/2022062516/56649e615503460f94b5c5ee/html5/thumbnails/8.jpg)
measurement cycle1) laser desorbed ionic biomolecules are introduced from one electrode of the trap
trap/TOF tandem leads to high mass resolution which can be extended to high m/q values allowing for the study of
large biomolecules.
1) reflectron2,3)
3) the trapping potentials are switched of
2) ions are accumulated and cooled
4)
4) a pulse of MCI passes the trapping region through the ring electrode
6) ions pass a reflectron TOF spectrometer
5)
5) a dc pulse applied to the second end cap extracts molecular ions and fragments
![Page 9: JRA3: Cold and Complex (Biomolecular) Targets Why study interaction of HCI with biomolecular targets? Basic physics: large energy transfer in a single](https://reader036.vdocuments.mx/reader036/viewer/2022062516/56649e615503460f94b5c5ee/html5/thumbnails/9.jpg)
C. Neutral gasphase bio-molecular targets
Target production via evaporation possible for DNA or RNA building bloks like thymine or uracil
Problem: Are the molecules in their electronic groundstate?
Approach for a solution: Check via reactions which are sensitive for electronic state
Example: H-loss or fragmentation in low energy attachment reactions
![Page 10: JRA3: Cold and Complex (Biomolecular) Targets Why study interaction of HCI with biomolecular targets? Basic physics: large energy transfer in a single](https://reader036.vdocuments.mx/reader036/viewer/2022062516/56649e615503460f94b5c5ee/html5/thumbnails/10.jpg)
Electron attachment (Scheier, Märk)
Thymine
Uracil
0 1 2 3 40
1
2
3
4
Electron energy (eV)
Cro
ss s
ectio
n (1
0-20 m
2)
(×0.33)
Glycine
M + e‾ → (M-H)‾ + H
P. Scheier, T. Märk
![Page 11: JRA3: Cold and Complex (Biomolecular) Targets Why study interaction of HCI with biomolecular targets? Basic physics: large energy transfer in a single](https://reader036.vdocuments.mx/reader036/viewer/2022062516/56649e615503460f94b5c5ee/html5/thumbnails/11.jpg)
D. Production and manipulation of ultracold targets
• Capture in magneto-optical traps (MOT’s)
• sympathetic cooling of molecules in a MOT
• Capture of biomolecules in He nano droplets
![Page 12: JRA3: Cold and Complex (Biomolecular) Targets Why study interaction of HCI with biomolecular targets? Basic physics: large energy transfer in a single](https://reader036.vdocuments.mx/reader036/viewer/2022062516/56649e615503460f94b5c5ee/html5/thumbnails/12.jpg)
Ultra cold Na target in a Magneto Optical Trap (MOT)
near resonance laser light to trap and cool Na atoms:
•Load from background vapor•106 –107 Sodium atoms•sub mm size cloud•200-300 K (<30 neV!)
laser light + magnetic quadrupole field = MOT
P P-hn
red detuned light
Spontaneous emission
![Page 13: JRA3: Cold and Complex (Biomolecular) Targets Why study interaction of HCI with biomolecular targets? Basic physics: large energy transfer in a single](https://reader036.vdocuments.mx/reader036/viewer/2022062516/56649e615503460f94b5c5ee/html5/thumbnails/13.jpg)
TOF and recoilspectroscopy of O6+ + Na collisions
-12 -10 -8 -6 -4 -2 0 2 40
10
20
30
40
50
60
70
80
90
100
110
tra
nsve
rsal
mo
me
ntu
m
longitudinal momentum-12 -10 -8 -6 -4 -2 0 2 40
10
20
30
40
50
60
70
80
90
100
110
tra
nsve
rsal
mo
me
ntu
m
longitudinal momentum
Na4+
-12 -10 -8 -6 -4 -2 0 2 40
10
20
30
40
50
60
70
80
90
100
110
tra
nsve
rsal
mo
me
ntu
m
longitudinal momentum
Na3+ Na2+
![Page 14: JRA3: Cold and Complex (Biomolecular) Targets Why study interaction of HCI with biomolecular targets? Basic physics: large energy transfer in a single](https://reader036.vdocuments.mx/reader036/viewer/2022062516/56649e615503460f94b5c5ee/html5/thumbnails/14.jpg)
Apparatus for He nanodroplet studiesToennies et al , Physics Today, Feb. 2001, 31-37
![Page 15: JRA3: Cold and Complex (Biomolecular) Targets Why study interaction of HCI with biomolecular targets? Basic physics: large energy transfer in a single](https://reader036.vdocuments.mx/reader036/viewer/2022062516/56649e615503460f94b5c5ee/html5/thumbnails/15.jpg)
Helium droplet beam Helium droplet beam machinemachine
Fakultät für PhysikFakultät für Physik
![Page 16: JRA3: Cold and Complex (Biomolecular) Targets Why study interaction of HCI with biomolecular targets? Basic physics: large energy transfer in a single](https://reader036.vdocuments.mx/reader036/viewer/2022062516/56649e615503460f94b5c5ee/html5/thumbnails/16.jpg)
Formation of large molecular complexes in helium Formation of large molecular complexes in helium dropletsdroplets
0.00.20.40.60.81.0 (PTCDA)
n in helium droplets
Rel
. Fl
uore
scen
ce
0.0
0.2
0.4
0.6
0.8
1.0
Abs
orpt
ion
PTCDA on quartz
17000 19000 21000 23000 250000.0
0.2
0.4
0.6
0.8
1.0 PTCDA monomer spectrum
Rel
. Fl
uore
scen
ce
Wavenumber [cm-1]
Formation of large molecular complexes in helium Formation of large molecular complexes in helium dropletsdroplets
M. Wewer and F. Stienkemeier, Phys. Rev. A 37, 2002
Spectroscopy of excitonic transitions in PTCDA nanostructures at 380 Spectroscopy of excitonic transitions in PTCDA nanostructures at 380 mKmK
![Page 17: JRA3: Cold and Complex (Biomolecular) Targets Why study interaction of HCI with biomolecular targets? Basic physics: large energy transfer in a single](https://reader036.vdocuments.mx/reader036/viewer/2022062516/56649e615503460f94b5c5ee/html5/thumbnails/17.jpg)
Laser induced fluorescence
spectrum of PTCDA
(a) in a nanodroplet (b) in the gasphase
F. Stienkemeier and A.F. VilesovJ. Chem. Phys.115 (2001) 10119
![Page 18: JRA3: Cold and Complex (Biomolecular) Targets Why study interaction of HCI with biomolecular targets? Basic physics: large energy transfer in a single](https://reader036.vdocuments.mx/reader036/viewer/2022062516/56649e615503460f94b5c5ee/html5/thumbnails/18.jpg)
E. Data reduction and analysis
A non-trivial task!
High-dimensional parameter space! (up to 30-40 parameters per collision event)
Pattern recognition
Fitting procedures based on e.g. maximum entropy methods
![Page 19: JRA3: Cold and Complex (Biomolecular) Targets Why study interaction of HCI with biomolecular targets? Basic physics: large energy transfer in a single](https://reader036.vdocuments.mx/reader036/viewer/2022062516/56649e615503460f94b5c5ee/html5/thumbnails/19.jpg)
2000
4000
6000
0 40 80 120
Xe20+ (400 keV)
Aq+
+ thymidine ( = 0°)
0
100
200
300
0 40 80 120
O2+ (40 keV)
mass/charge (a.u.)
cou
nts
Xe20+, 400 keV
O2+, 40 keV
Huber et al, Caen
NIM B 205 (2003) 666–670
Fragmentation of thymidine by ions with high and low
charge