Comparison of x-ray and electron beams for structural, chemical

and elemental analysis

R.F. EgertonPhysics Department, University of Alberta,

Canada

regerton@ualberta.ca

www.TEM-EELS.com

Structural analysis by x-rays and electrons

Hard x-ray diffraction and diffractive imaging structure

X-ray absorption fine structure (EXAFS, NEXAFS) structure

Soft x-ray absorption in water window elemental or chemical map

Electron diffraction and diffractive imaging (100 – 300 keV) structure

TEM scattering-contrast imaging (amplitude contrast) structure

TEM phase-contrast imaging (obj. defocus or phase plate) structure

STEM annular dark-field (ADF) imaging structure, Z-contrast image

Electron energy-loss imaging elemental map etc.

Electron energy-loss spectroscopy composition, structure

I0

Plasmon

Co M23 Nucleus

corelevels

valenceband

conductionband

e-

e-

Echenique et al, PRB 20 (1979), p. 2567

potential

charge

dielectric

Single e-

e-

b

Electron Energy-Loss Spectrum

Some practical considerations

X-ray synchrotrons TEM + EELS, EDX spectroscopy---------------------------------------------------------------------------------------------

< 10 sites in USA several major centers + many routine instruments

Zone–plate focusing to Focusing to < 0.1 nm20nm with ~ 5% efficiency with 100% efficiency

Detectable concentration Detectable mass < 10-20 g< 1 ppm by fluorescence

Micron-thick specimens Specimens < 500 nm thick(but overlap of structure) (spec. prep. time-consuming)

Environmental cells easy Environmental cells difficultbut feasible with MEMS

Recording time ~ hours Recording time ~ secs, mins

X-rays and electrons are ionizing radiation:

X-ray absorption photoelectrons radiolysis

Electron inelastic scattering secondaries radiolysis(PMMA: > 80% of radiolysisis due to secondaries)

How electrons differ from x-rays:

They have charge efficient focusing by magnetic lenses but Coulomb repulsion limitation on incident fluxAlso, electrostatic charging of insulating specimens (rupture) deflection of incident and imaging beam (microlensing)

Electrons have rest mass and appreciable momentum knock-on displacement damage Energy transfer few eV or tens of eV for high-angle scatteringBut this is rare, so knock-on damage is mainly observed in conducting specimens, where radiolysis is absent.

Effects of knock-on damage (conducting specimen):

Atom displacement in the bulk (Ed ~ tens of eV)

Atom displacement at grain boundaries (Ed ~ few eV)

Atom displacement from a surface (e-beam sputtering)

Atom displacement along a surface (radiation-enhanced diffusion)

Decreasing displacement energy Ed

and decreasing incident-energy threshold.

For 180° scattering, E0th = (511 keV)[1+AEd/561eV] 1/2 - 1]

Graphite irradiated by 200keV electrons for10 minutes at 600C (Dose ~ 500 C/cm2)

Egerton, Phil. Mag. 35 (1977) 1425.

material Ed(eV) Eth(keV)

diamond 80 330

graphite 34 150

aluminum 17 180

copper 20 420

gold

MgO3460

1320330,460

Bulk (volume) displacement atomic clusters

Simulation of neutron damagein nuclear fuel rods etc.

Electron-induced sputtering

incidentelectron

entrancesurface

exitsurfacehigh-angle ‘elastic’

collisions witha single atom

incidentelectron

Inside specimen, can create interstitials and vacancies

Calculated cross sectionsfor e-sputtering

No effect below threshold energy.

Thinning rate(monolayer/s)= (J/e) ~ 10for = 100 barn

and J =104A/cm2

(10pA in 1nm2)

J >106 A/cm2 forCFEG & Cs-corr.

Spatial resolution of imaging and spectroscopy

Electrons have small deBroglie wavelength (<< 0.1 nm for E0 > 15 keV) and can be focused efficiently by electromagnetic lenses

High spatial resolution in imaging, diffraction and spectroscopy, as in the (S)TEM.

Electron lenses have high spherical and chromatic aberration but these aberrations can now be corrected.

Instrumental resolution ~ 0.05 nm for E0 ~ 200 keV.

This is the practical resolution for conducting (e.g. metal) specimens

where knock-on displacement (inefficient) is the only damage mechanism

Ionization damageversus knock-ondisplacement in organic samples

Microscopy Research & Technique75 (2012) 1550

Non-conducting (e.g. organic) specimens

Resolution is limited by ionization damage (radiolysis)

Dose-limited resolution (SNR) C-1 (DQE. F.Dc/e)-1/2

SNR ~ 3 to 5 (Rose criterion)

C = contrast between resolution elements

DQE = performance of recording system

F = specimen/detector attenuation (e.g. TEM objective aperture)

Dc/e = critical dose in electrons/area

Calculated contrast C and dose-limited resolution for a boundary in polymer (projected structure, 10% density change)

TEM bright-field scattering contrast

Resolution improves with increasing thicknessuntil F becomes small

(most electrons absorbed

by objective aperture)

Low kV is better for a very thin specimen( ~ C-1Dc

-1/2) but worse for thicker one.

Calculated contrast C and dose-limited resolution for 10% density change in a polymer (e.g. PMMA)

Phase contrast

Contrast and resolution both improve with increasing thickness,until the phase shift exceeds 3/4.

For thin specimens,

~ Cph -1 Dc-1/2 ~ E0

1/2 E0-1/2

i.e. independent of kV, buthigher kV allows thicker specimen -> smaller .

Assumes an ideal phase plate (future possibility)

overlap problems

Dark-field imaging in scanning mode (ADF-STEM)

Pennycook, Condensed Matter Physics (2005)

ADF-STEM imaging of a polymer (10% density change)

Resolution versus inner detector angle Resolution versus incident energy

Three-dimensional imaging with x-rays or electronsvia tomography or diffractive imaging

Required dose less for electrons due to stronger elastic scatter (Henderson etc.)

Damage dose (in Gray) same for electrons and x-rays (ionization damage)

Figure modifiedfrom Howells et al.JESRP 170 (2009)

Damage data fromDP fading forcalalase, proteinpurple membrane,bacteriorhodopsin,ribosomes etc.(Glaeser et al.,Howells et al.)

TEM cryo-microscopy of organics:

Repeated structure (e.g. crystal) lowers the required dose

atomic resolution in phase-contrast images

except for mechanical distortion and electrostatic charging of the specimen

Brilot et al.JSB (2012)

5nm

direct-e camera5 frames/sec

Li et al.Nat.Meth10 (2013) 584

X-ray direct imaging: resolution restricted to ~ 20nm (zone plate)

Diffractive imaging capable of atomic resolutionbut DLR is limited by radiation damage (e.g. 10nm) unless damage can be outrun (<100fs pulses)

Pulsed-laser-activated photoemission electron source

Short electron pulses, down to single electrons (Zewail)Used to studySolid-state phase transitionsMetal-insulator transitionNucleation and crystallization dynamicsNanomechanical systemsSurface-charging effectsPlasmonics in nanostructuresDynamics of chemical reactions

Free-electron laser gives femtosecond x-ray pulses

Short-pulse x-ray diffraction:

H. Chapman et al., Nat. Phys. 2 (2006) 839 25fs pulse containing 1012 photons (2.9keV, 0.32nm) gives a diffraction pattern of a patterned Si3N4 membrane before vaporizing it at 60,000 K.

Chapman et al. Nature 470 (2011) 7310fs, 70fs and 200fs pulses of 1.8keV (0.7nm) x-rays focused to 7 microns (900 J/cm2, dose = 700MGy/pulse)give DPs of a membrane-protein complex (size ~ 10nm)and demonstrate no damage below 70 fs (see below)

30MGydamages

cooled protein

Chapman et al. (2011)

Liquid-jet injector andpnCCD detectors (30Hz)

Photosystem-1 protein image

reconstructed fromfrom 15,000 DPsby coherent diffractive imaging

DP’s from detectors

Conditions for damage-free diffractive imaging

1. Flux high enough to generate sufficient signal before the object is destroyed.

2. Many objects can be used, improving the signal (as in a crystallized object) but for randomly-oriented objects the statistics in each DP must be adequate (e.g. 5000 diffracted photons, maybe less with sophisticated software).

3. Photoelectrons may escape from a small isolated object, making damage less than in an extended crystal.

4. Pulse length < 200 fs for efficiency. Nuclear motion (damage) occurs after about 30 fs, so the diffraction pattern gets blurred, then electrons arriving after destruction contribute nothing to the DP background.

5. For diffractive imaging, X-ray beam must be coherent over a diameter ~ particle size or over unit cell (for a crystalline object).

Can we do the same with electrons?

1.6-cell rf photocathode gun(BNl/SLAC/UCLA)

100fs electron pulses, with 106 -108 electrons/pulse.

Instantaneous current = 1.6 – 160 Amp

Problems: 1. Electron momentum (knock-on damage, negligible compared to ionization damage)

2. Electron charge:

Coulomb repulsion effects (Kruit & Jansen, 1997):

A. Space charge (effect on one electron of all others) compensate by refocusing

B. Trajectory displacement (statistical, between electrons) unavoidable

C. Energy broadening (Boersch-effect) increases chromatic aberration

Continuous beam (100keV electrons focused over 0.2m)

Current density limited to ~ 2000 A/cm2

Continuous beam (2.5MeV electrons focused over 0.2m)

Maximum current density now ~ 65 MA/cm2

Pulsed electron beam: if Coulomb repulsion same,2.5MeV dose within 100fs = (1e-13)(65e6) = 6e-6 C/cm2

2.5MeV damage dose ~ 6e-2 C/cm2 So negligible damage in a single pulse, short pulses may offer no advantage.

Kruit & Jensen equations include relativistic factor: V* = V(1+eV/m0c2),but not magnetic attraction of parallel-trajectory electrons: Ftotal = (e/20)(/2)r

Also, Coulomb repulsion in a short pulse may be less. So the above dose estimates will be too low.

Relativistic particle-bunch calculations are needed.

Is it necessary to outrun primary damage (fs time scale) ?

1. Short x-ray pulses needed only to increase collection efficiency

2. Secondary damage has longer timescales.

Radiolysis time scale (Warkentin et al. 2012)

Secondary damage can be avoided if structural information is acquired on a nanosecond to millisecond time scale .

This requires:

Fast detectors Efficient signal collectionSlow down secondary processes e.g. by cooling specimen

The existence of these longer time scalesimplies a dose-rate dependence of the damage dose Dc.

Dose-rate dependence of damage by x-rays

Change in damage dose reflects free-radical secondary damage

Warkentin et al.Acta Cryst.(2013)

Evidence for dose-rate effects in electron-irradiation of organic materials

Wery & Mansot, Microsc. Microanal. Microstruct. 4 (1993) 87. Formation of f.c.c. lead (detected indiffraction pattern) in lead isooctanoate.

Egerton and Rauf, Ultramicroscopy80 (1999) 247. Loss of O,C and Nfrom collodion at 90 K.

++ _

computersimulation

Suggests that STEM can “outrun” mass loss (less damage in elemental map)if probe current not high enough to cause appreciable temperature rise

Simulation for 1nm electron probe (as in STEM):

dose De for mass loss from organic polymerat 90 K

Conclusions

Electrons and x-rays and electrons are both ionizing radiationRadiation damage higher for EXELFS than for EXAFS

Damage may be less for elastic imaging by electronsbecause electrons are scattered more strongly

very thin specimens, sometimes difficult image interpretation sometimes more complicated

Electron beams can be focused down to 0.1 nm very small analysis volume

Energy resolution of EELS and XAS now comparable (0.01 – 1 eV)

Femtosecond imaging/spectroscopy more difficult with electronsbut cryo-TEM can now achieve atomic resolution from small organic crystals and large macromolecules.

Henderson, Quart. Rev. Biophys. 2 (1995) 171

Electrons soft x-ray hard x-ray--------------------------------------------------------------------------------------------------

Energy/inelastic event 20 eV 400 eV 8 keV

Energy/elastic event 60 eV 400 keV 80 keVIf the signal is elastic, X-rays are 104 to 105 times more damaging

Protein/water contrast 0.4 10X-ray water-window contrast 25 times higher than in TEM-BF image

This factor outweighs the noise advantage of BF-TEM: (400/60)1/2 = 2.6but TEM phase contrast ~ 40 times more contrast than BF (TMV in ice),giving (2.6)(40)/25 ~ x 4 advantage for electrons

In practice, TEM resolution of biomolecules is often limited by beam-induced specimen movement and charging (micro-lensing).

Radiation units

X-ray community (and most radiation specialists) measure radiation dose in terms of deposited energy,in units of Gray (= J/m3) or MegaGray (MGy)

Electron microscopists use “dose” = fluence = (beam current density)(time) = Coulomb/cm2

or particles/area , usually e/nm2 or e/Angstrom2

1 C/cm2 [104 / IMFP(nm)] [Eav(eV) / (g/cm3)]

For 100keV electrons and typical organic material, IMFP ~ 100 nm, Eav ~ 35 eV and ~ 1.4 g/cm3, giving 1 C/cm2 2500 MGyor 1 electron/Angstrom2 4 MGy

Critical or characteristic dose Dc:Amino acid (l-valine): 0.002 C/cm2 , 5 MGyChlorinated Cu-phalocyanine: 30 C/cm2, 75 GGy

Usual assumption: damage proportional to accumulated dose(critical dose is independent of dose rate).This is the basis for using Gray or rad units

Primary process leading to damage: < 1 fs absorption (x-rays) or inelastic scattering (electrons) core- or valence-electron excitation (single-electron or plasmon) bond breakage (may not be permanent, damage not 100% efficient) creation of photelectrons or secondary electrons, Auger electrons

Secondary processes: additional damage created by secondary electrons (~80% in PMMA)or photoelectrons (predominant damage process for hard x-rays)------------------------------------------------------------------------------------------------motion of atomic nuclei, leading to structural damage > 50 fs(thermal motion may contribute temperature dependence of damage)

Tertiary processes include: ns, ms, s, days...Loss of crystalline structureDiffusion from or into the irradiated area (composition change)Escape of material form the specimen (mass loss) Dielectric breakdown due to charge buildupDisruption of biological processes (e.g. cell death)

These slower processes may nonlinear dose-rate dependence of damage

Classification of dose-rate effects

Diffusion leads to mass loss or precipitation, expect positive d-r effectFast XFEL pulses allow diffract & destroy (Chapman et al., 2011) positiveDiffusion allows recovery (Jiang & Spence, 2012) negative, threshold

Beam heating causes mechanical motion (Downing, 1987) negativeor faster radiolysis in polymer (Beamson; Egerton & Rauf) negative

Electrostatic charging causes dielectric breakdown or Coulomb explosion hole formation in oxides (Humphreys et al.) negative, threshold

Implications:STEM, STXM give high dose rate for short dwell time.Scanning is beneficial if the dose-rate effect is positive.

Diffusion effects continue after irradiation: better to scan once only[wet chromosomes, Williams et al. J. Microsc. 170 (1993) 155 ]

Scanning is detrimental if the dose-rate effect is negative.Fixed-beam microscopy could then give less damage for the same information.

100keV electrons and 100fs pulses:

Current density ~ 4e9 A/cm2, dose ~ 4x10-4 C/cm2 per pulse

Electron energy 30fs-dose damage dose (1nm, protein)- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 100 keV 0.3 Mgy 100 MGy

2.5 MeV 3 Mgy 300 MGy

30fs-dose is below CW damage threshold for most organicsSo many pulses required for good spatial resolution

No advantage over CW irradiation unless short pulses fail to excite lattice motion.

Calculations include relativistic factor: V* = V(1+eV/m0c2), but notmagnetic attraction of parallel-trajectory electrons: Ftotal = (e/20)(/2)rSo the above dose estimates are likely too low.

In practice, other factors can limit the beam diameter:Spherical aberration, chromatic aberration, diffraction limit,geometric source size ( ~ 100m in BNL apparatus, reduced by focusing the laser illumination or using a small emitter tip)