Electron induced chemistry – applications from Astrochemistry to cancer therapy Nigel John Mason.

Electron induced chemistry –applications from Astrochemistry to

cancer therapy

Nigel John Mason

Electron Induced Processes

Atmospheric physics and planetary atmospheres


Astrochemistry: Formation of molecules in Space


Semiconductor plasmas


Lighting industry


Radiation damage of DNA and cellular material

Electron Induced Processing

Nanotechnology and surface engineering

Electron Induced Chemistry;

In this presentation I will describe;

• The role of low energy electrons in electron driven chemistry

• Show how such research can be applied to study fundamental problems in natural and industrial world

In Europe this research has been developed through collaborative programme Funded by EU

2002 Framework V Network EPIC 2002-2005 Electron and Positron Induced Chemistry

EU COST Action P9 RADAM Radiation damage 2004-2007

ESF Programme Electron Induced Processing at the Molecular Level (EIPAM) 2004-2009

EU COST Action CM0601 Electron Controlled Chemical Lithography 2008-11

EU COST Action CM0805 Astrochemistry 2009 - 2013

Electron Based research in Europe

http://physics.open.ac.uk/epic/intro.html

How do electrons trigger chemistry ?

By

• Exciting

• Dissociating or

• ionising molecules

with subsequent products being reactants in collisional chemistry

Electron Induced Chemistry; Chemical Control at the Molecular Level

Consider for example simple electron induced dissociation through an excited molecular electronic state.

e- + M M# X + R + e (1)

R + AB AR + B (2)

Example 1

Formation of glycine in the Interstellar medium


Example: Glycine in the ISM ?

• Kuan et al 2003 – The Astrophysical Journal,

593:848–867, 2003

• Searched for interstellar conformer I glycine (NH2CH2COOH), the simplest amino acid, in the hot molecular cores Sgr B2(N-LMH), Orion KL

• ALMA will search/dectect for Glycine

Kleinman-Low (KL) Region of the Orion NebulaSubaru Telescope, NAOJ

To pumping station

Continuous flow cryostat Ion gauge

Cryogen inlet via transfer line

Temperaturecontroller

Sources

E-gun

Synchrotron

Ion Source

Resistive heater

ThermocouplesMgF2/ZnSe

substrate

Copper sample mount

Detectors

- UV-VIS / FTIR detector

- Photomultiplier Tube

Sources- UV-VIS / FTIR

spectrometer- Synchrotron

• Vacuum chamber to mimic empty space:

– P~10-8 - 10-10 mbar• Still > a million times higher

than ISM!

• Temperature very cold in space– Continuous flow LHe/LN2

cryostat• 12 K < T < 450 K

• Material to mimic grains

• Make ice Samples

• Use spectroscopy to see what you make

Experimental Procedure

• Ice sample was prepared at 10 K by depositing binary gas mixtures of methylamine (CH3NH2; and carbon dioxide (CO2) onto a cooled silver crystal.

• Ice thickness & column densities determined by Beer-Lambert Law

• Column densities of carbon dioxide and methylamine of

2.00.4 1016 cm-2 and 7.20.21017 cm-

2 respectively

5 keV Electron irradiation of methylammine and carbon

dioxide ice makes glycine simple amino acid

05th Jan 2006 Chemistry of Planets

Electron Induced Chemistry

• Some examples of laboratory study of electron induced synthesis of molecules under astrochemical conditions.

• Chemical synthesis in 1:1 Mixture of NH3:CO2 Ice with 1 keV electrons at 30 K


Formation of ammonium carbamate


Electron Induced Chemistry

• Some examples of laboratory study of electron induced synthesis of molecules under astrochemical conditions.

• Chemical synthesis in the Irradiation of 1:1 Mixture of NH3:CH3OH ice with 1 keV electrons at 20 K


Formation of ethylene glycol in pure methanol ice

HOH2C-CH2OH


Formation of methyl formate CH3OHCO


Formation of formamide HCONH2

(Khanna, Lowenthal et al. 2002)


These are examples of high energy electrons ‘Blasting’ molecules apart or release of secondary electrons !!

But at low energies electrons can do surprising things !


At low energies electrons can do surprising things !

• They can ‘stick’ to the molecule • To form a negative ion or ‘resonance’ • But only for a very short period of time (10-14 s)

• Then the electron detaches • Leaving molecule excited or not (elastic scattering)• But this process can also lead to the dissociation of the molecule

This is the process of Dissociative Electron Attachment (DEA)

Bond Selectivity using Electrons

Process of Dissociative Electron Attachment


Dissociative electron attachment therefore

provides a method for breaking up molecules

at low energies

Energies lower than the chemical bond energy !!!

Hence electrons can initiate chemistry

Electron Induced chemistry

• Electrons used to ‘tune’ the products of a reaction

• Through selective bond dissociation different energy different pathways



Selective C-Cl bondcleavage at 0 eV

Selective C-F bondcleavage at 3.2 eV

Illenberger et al Berlin

Nucleophilic Displacement (SN2) Reaction

e.g. : F- + CH3Cl CH3F + Cl-

e- + CH3Cl CH3 + Cl-

< 10-23 cm2 (unmeasurably small)

fromimpurity

SN2 Reaction

Illenberger et al Berlin

(NF3)n•(CH3Cl)m

CH3Cle-

e-

e-

no ions

F-

Cl-

• Chemical surface transformations using electron induced reactions/

• DEA produces products that subsequently react on the surface

• E.g. Irradiate film of NF3 and CH3Cl

• Form CH3F

e-

F-

CH3Cl CH3F

Cl-

R. Balog and E. Illenberger

Phys. Rev. Letters 91 213201-1

• Complete chemical

Transformation

of thin films

e + C2F4Cl2 → C2F4 + Cl2

C2F4 desorbs

So surface transformation

to 100% Cl2 film !!Cl2

Basice--moleculeinteractions

Resonances

E0 dependence

Control via e--induced chemistry developing electron lithography

e--induced chemistry

Cross sections

Typical reactions and products

Reaction sequences

Surface functionalization

Reactionsat the interface

of materials

Modification of materials properties

- structural- electrical- permeability- optical

Functionalization of H-diamond

CH3CN / H-diamond at 35 K, E0 = 2 eV

0 100 200 300 400 500

(d)

(c)

(b)

(1a)

Inte

nsi

ty (

a.u

.)

Energy Loss (meV)

C. Jäggle

Cooperation:R.Azria and A.Lafosse

e-(E0)

CH3CNH HH HH H

H HH HH H

HCH

2C

N

HH HNC

CH

2

DEA and biomolecules

• DEA is a universal process

• So DEA will occur in biomolecules including those constituents of DNA

• So can DEA induced fragmentation lead to DNA damage ?

In many molecules DEA leads to H atom loss

• This is most dominant process in DEA to organic acids

• E.g. acetic, formic and …

Relative cross sections of H Relative cross sections of H channel channel for Carboxylic acidsfor Carboxylic acids

0 2 4 6 8 10 12 14 16 18

0 2 4 6 8 10 12 14 16 18 0 2 4 6 8 10 12 14 16 18

0 2 4 6 8 10 12 14 16 18

8.6eV

6.5eVWater

6.6eV9.1eV

7.3eVFormic Acid

9.1eV

7.7eV

6.7 eVAcetic Acid

6.7eV 9.1eV

7.7eVPropionic Acid

Electron energy (eV)

Ion

cu

rren

t

O

HCC

H

H

OH

O

HCC

H

H

OD

CHCH33COODCOOD

0 2 4 6 8 10 12 14 16 180 2 4 6 8 10 12 14 16 18


H/ CH3COOH

H/ CH3COOD

D/ CH3COOD


H/ CH3COOH

CHCH33COOHCOOH

Prabhudesai et al. PRL (2005)

Is this unique for carboxylic Is this unique for carboxylic acids?acids?

0 2 4 6 8 10 12 14 16 180 2 4 6 8 10 12 14 16 18

0 2 4 6 8 10 12 14 16 18

9.6eV

6.3eVEthanol

10.1eV7.9eV

6.4eVMethanol

8.6eV

6.5eV Water

CH3OH CH3CH2OH

H H from Amine from AmineH / CH4

H / NH3

0 2 4 6 8 10 12 14 16 18Electron energy (eV)

n-Propyl amine

CH3CH2CH2NH2

or X e-

<20 eV

Single and double strand breaks may be induced by secondary

species: a large number of secondary electron with kinetic energies

below about 20 eV, are produced along the radiation track

Damage of the genom in living cell by ionising

radiation is about 1/3 a direct and 2/3 an indirect

processes.

Radiation damage to DNA

Can electrons damage DNACan electrons damage DNA??

super coiled DNA

single strand break SSB

double strand breakDSB

DNA damage - strand breaks

Mechanisms for ssb and dsb induction at low-energies

• Boudaiffa et al. (Leon Sanche, Sherbrooke Canada) demonstrated that there apperas tpo be a corrrelation between patterns of ssb and dsb induced in DNA and DEA of constituent molecules

Resonant Formation of DNA Strand Breaks by Low-Energy (3 to 20eV) Electrons. Science 287, 1658-1660 (2000). B. Boudaiffa, P. Cloutier, D. Hunting, M.A. Huels et L. Sanche.

L. Sanche et al. Science, 287 (2000) 1659 and PRL (2004)

Strand breaks of DNA

10

0 5 10 15 20

0

5

10

SSB DSB

Electron Energy (eV)

DN

A b

reak

s pe

r 10

4 in

cide

nt e

lect

rons

L. Sanche et al. Science, 287 (2000) 1659 and PRL (2004)

Strand breaks of DNA

10

0 5 10 15 20

0

5

10

SSB DSB

Electron Energy (eV)

DN

A b

reak

s pe

r 10

4 in

cide

nt e

lect

rons

e- + DNA → DNA-* → fragments

DNA – deoxyribonucleoside acid

ion beam

neutral beam

electron beamFWHM ~ 100 meVIe ~ few nA

Hemispherical electron monochromator

oven

quadrupole mass spectrometer

channeltron

~ 150°C~ 10-7 mbar

Experimental setup – gas phase Innsbruck

Thymine + e- → TNI-* →electron attachment

C5H6N2O2-

e-dissociative electron attachment

(T-H)- + H(T-2H)- + neutral(s)

C4H5N2O- + neutral(s)

C2H3N2O- + neutral(s)

C3H2NO- + neutral(s)

CN- + neutral(s)

O- + neutral(s)H- + neutral(s)

OCN- + neutral(s)

→→→

→→

→C3H4N- + neutral(s)

→

→

→

→

Dissociative Electron Attachment

126 amu

125 amu

124 amu

1 amu

16 amu

26 amu

42 amu

54 amu

68 amu

99 amu

73 amu

0 1 2 3 40

2

4

6

8

10

12

Cro

ss s

ectio

n (1

0-20 m

2)


H loss

e-

Electron Attachment to Thymine

(M-H)-

125 amu

0.4

0

0.7

Δ#,1

1.4

binding energies of C-H and N-H bonds

electron affinities of various (U-H) isomers

1.3

0.9

1.6

Emin

2.3

1

3

5

6

#

1

23 4

5

6

4.3 eV 5.0 eV

4.5 eV

5.8 eV-4.5 eV

-3.4 eV

-2.9 eV

-2.7 eV

C

C

C

CO

N

O

N

C

C

C

C

CO

N

O

N

C

e-

Quantum Chemical Calculations

Thymine-methyl-d3-6-d

5-methyluracil

1-methylthymine Uracil 3-methyluracil

Thymine

Carbon

Nitrogen

Oxygen

Hydrogen

Deuterium

Thymine-methyl-d3-6-d

5-methyluracil

1-methylthymine Uracil 3-methyluracil

Isotope and site labelling thymine

0 1 2 3

0

20

40

60

80

100

Io

n s

ign

al (

arb

. un

its

)


(M-H)-

m1T

m3U

1

3

Site and bond selectivity in DEA

129 amu

GCAT

GCAT

G+C+A+TG+C+A+T

EA - electron affinityEA(CN)= 3.82 eVEA(CNO)= 3.61 eV

DEA to oligomers

O

PO-

NH2

N N

NNHO O

O

O

NH2

O

N

N

P

OO OO-

O

O NH2

N

N

N

N

NN

O

O

O

OO

O

O-

O

OH

G

C

A

Toligomertetramer

(1172 amu)

P

CN- CNO-Gas phase

Condensed phase

Does DEA explain effectiveness of some radiosensitizers ?

• Observation of correlation between carcinogens and DEA rates ?

• Effectiveness of halogenated compounds as radiosensitizers

Uracil Thymine Bromouracil (Radiosensitizer)

(UCl)-

(UCl-HCl)-

0

2

4

6

8

10

0 1 2 3 40

100

200

300

400

500


0

50

100

150

200

250

Cro

ss s

ecti

on

(Å

2 )

(Cl)-

Ratios: X-/(U-yl)- = 1.3, 40, 490 (X=Cl,Br,I) Present: Cl-/(U-yl)- =0.47

Halo-uracils measured by Illenberger et al Berlin.UCl + eUCl + e-- anionsanions

+ Br

.

≈ 600 Å2

Freie University Berlin

New techniques for electron scattering!

The Method of Scanning Tunnel Microscopy

Electron current from fine metal tip interacts with (metal) substrate

Electron Induced Chemistry; Nanotechnology


www.eng.yale.edu/.../ spm/stm-operation.gif

STM

M

e-

Single Molecule Engineering

• Changing environment like temp., pressure or catalyst

• Coherent pulse sequence – (Potter et.al. Nature 355, 66 (1998))

• Optimal control by shaping of fast pulses – (Levis et.al. Science 292, 709 (2001))

• Addressing single molecule using STM – (Pascual et al. Nature 2003, Sloan and Palmer,

Nature 2005)

Optimal control using laser pulse shapingOptimal control using laser pulse shapingActive control of chemical reactions

Nature, 2003

Making new molecules

Hla et al (Berlin)

C12H10



Chemical Control at the Molecular Level

Nature 434, 367-371

Two-electron dissociation of single molecules by atomic manipulation at room temperature



Electron excitation and dissociation of individual oriented chlorobenzene molecules on a Si(111)-7 7 surface at room temperature by a two-electron mechanism that couples vibrational excitation and dissociative electron attachment steps.

The first electron interacts with the chlorobenzene molecule; the molecule is left vibrationally excited (specifically, the C−Cl wag mode is excited); the second electron interacts with the molecule before the C−Cl wag mode has fully relaxed, leading to dissociation of the C−Cl bond by DEA;

Focussed Electron and Ion Beam Deposition

So What Next ?????

• Plans for 2011-14 (in Europe)

1.Negative ions in plasmas. Use to tune fragmentation pathways in semiconductor plasmas.

2.Anions may be used to form radicals for surface chemistry.


• Plan for 2011-14 (in Europe)

1. Tune fragmentation pathways in semiconductor plasmas. Negative ions in plasmas programme Europe with Japan.

2. DEA as a process for nanolithography (electron/positron and photoelectron processing). Surface engineering using STM to manipulate molecules EU programme


• Plan for 2011-14 (in Europe)


2. DEA as a process for nanolithography (electron/positron and photoelectron processing). Surface engineering using STM to manipulate molecules

3. Electron damage of biomolecules and DNA (electron transport in DNA nanowires).NEW COST IBCT Action


Plan for 2010-14 (in Europe)


2. DEA as a process for nanolithography (electron/positron and photoelectron processing). Surface engineering using STM to manipulate molecules EU programme (with Australia).

3. Electron damage of biomolecules and DNA ( electron transport in DNA nanowires) EU Programme.

4. Astrochemistry; low temperature electron processing of ices to probe molecular formation in space;


Collaborative programmes (Europe)

ESF/COST Electron Controlled Chemical Lithography 2007-10

ESF/COST The Chemical Cosmos 2009-2013

ESF/COST IBCT 2010-14

EU Research Infrastructure Europlanet 2009 -2012

EU Initial Training Network LASSIE 2010-14

VAMDC atomic and molecular database 2009-2012

COST is supported by the EU RTD Framework Programme

ESF provides the COST Office through an EC contract

VAMDC

• A database of Atomic and molecular data for applications including astronomy.

• Http://www.vamdc.org/

Role for Quantemol

• This range of applications requires a lot of data !

Data overload ?Data overload ?

DatabasesDatabases Assembly, Assembly,

intercomparisointercomparison, n, error/sensitiviterror/sensitivity analysisy analysis

Quantemol NQuantemol N

Calculate cross sections ! But low Calculate cross sections ! But low energy so..energy so..

Combine with higher energy (India, Combine with higher energy (India, Vinodkumar. Joshipure, Antony) Vinodkumar. Joshipure, Antony)

Zero to 1000s eVZero to 1000s eV



0.1 1 10 100 10000

10

20

30

40

50

60

TC

S2إ) )

Ei(eV)

Present Qmol Present SCOP Zecca Soeoka Garcia Ariyasinghe szmytkowski Alle Liu ADR Liu SEF Munjal Gianturco

e - NH3



0.1 1 10 100 1000

0

10

20

30

40

50

60

70

TC

Sإ)

2)

Ei(eV)

Present Qmol Present SCOP Szmytkowski Munjal Bettega J ain

e - PH3

Quantemol Quantemol

Ca n estiamte cross sections for Ca n estiamte cross sections for targets experimrntalists don’t want targets experimrntalists don’t want to touch ! Or cant do to touch ! Or cant do

Radicals ( CFRadicals ( CFxx SiH SiHxx OH CCCH etc) OH CCCH etc)

But challenge for larger systems But challenge for larger systems DyIDyI33

The team – with thanks UCL and OU • Sarah Barnett, Julia Davies, • Jon Gingell, Andy Birrell,• Nykola Jones, Petra Tegeder• Paulo Vieira, Samuel Eden, • Paul Kendall, Anita Dawes• Philip Holtom, Robin Mukerji,• Dagmar Jaksch, Mike Davis, • Sarah Webb, Liz Drage, • Eva Vasekova, Gosia Smialek, • Bhala Sivaraman, Sohan Jeetha• Patrick Cahillane, William

Stevens.

Sylwia Ptasinska, Sam Eden, Jimena Gorfinkiel, Radmila Panajatovic

And finally to all my colleagues– with thanks

• Tilmann Märk, Paul Scheier et al , Universität Innsbruck, Austria• David Field, Nykola Jones,Soren Hoffmann University Aarhus,

Denmark • Eugen Illenberger and group Frei University Berli• Stefan Matejcik, Jan D. Skalny, Comenius University, Bratislava• Gustavo Garcia, Madrid, Spain• Paulo Vieira Lisbon. Portugal• Marie Jeanne Hubin Franskin, Jacques Delwishe, Liege, Belgium • K Joshipura and M Vinodkumar Sarad Patel university India• B Raja Sekhar CAT Indore and BARC India• H Tanaka Sophia Univeristy Tokyo and Y Itikawa , Japan

• And all those others in our EU Collaborations

http://www.isa.au.dk/epic/intro.html

Electron induced chemistry – applications from Astrochemistry to cancer therapy Nigel John Mason.

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