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

Comparison of x-ray and electron
beams for structural, chemical
and elemental analysis
R.F. Egerton
Physics Department, University of Alberta,
Canada
[email protected]
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
econduction
band
Electron Energy-Loss Spectrum
I0
valence
band
core
levels
Plasmon
Single e-
Co M23
Nucleus
b
e-
potential
e-
charge
dielectric
Echenique et al, PRB 20 (1979), p. 2567
Some practical considerations
X-ray synchrotrons
TEM + EELS, EDX spectroscopy
---------------------------------------------------------------------------------------------
< 10 sites in USA
several major centers +
many routine instruments
Zone–plate focusing to
20nm with ~ 5% efficiency
Focusing to < 0.1 nm
with 100% efficiency
Detectable concentration
< 1 ppm by fluorescence
Detectable mass < 10-20 g
Micron-thick specimens
(but overlap of structure)
Specimens < 500 nm thick
(spec. prep. time-consuming)
Environmental cells easy
Environmental cells difficult
but 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 flux
Also, 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 scattering
But 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]
Bulk (volume) displacement
material
Ed(eV)
Eth(keV)
diamond
80
330
graphite
34
150
aluminum
17
180
copper
20
420
gold
34
1320
MgO
60
330,460
Simulation of neutron damage
in nuclear fuel rods etc.
 atomic clusters
Graphite irradiated by 200keV electrons for
10 minutes at 600C (Dose ~ 500 C/cm2)
Egerton, Phil. Mag. 35 (1977) 1425.
Electron-induced sputtering
incident
electron
incident
electron
entrance
surface
Inside specimen, can create
interstitials and vacancies
high-angle ‘elastic’
collisions with
a single atom
exit
surface
Calculated
cross sections
for e-sputtering
No effect below
threshold energy.
Thinning rate
(monolayer/s)
= s(J/e) ~ 10
for s = 100 barn
and J =104A/cm2
(10pA in 1nm2)
J >106 A/cm2 for
CFEG & 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 damage
versus knock-on
displacement in
organic samples
Microscopy
Research &
Technique
75 (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 d for a
boundary in polymer (projected structure, 10% density change)
TEM bright-field
scattering contrast
Resolution improves
with increasing thickness
until F becomes small
(most electrons absorbed
by objective aperture)
Low kV is better for a
very thin specimen
(d ~ C-1Dc-1/2) but
worse for thicker one.
Calculated contrast C and dose-limited resolution d
for 10% density change in a polymer (e.g. PMMA)
Phase contrast
Assumes an ideal phase plate (future possibility)
Contrast and resolution
both improve with
increasing thickness,
until the phase shift
exceeds 3p/4.
For thin specimens,
d ~ Cph -1 Dc-1/2 ~ E01/2 E0-1/2
i.e. independent of kV, but
higher kV allows thicker
specimen -> smaller d.
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 electrons
via tomography or diffractive imaging
Figure modified
from Howells et al.
JESRP 170 (2009)
Damage data from
DP fading for
calalase, protein
purple membrane,
bacteriorhodopsin,
ribosomes etc.
(Glaeser et al.,
Howells et al.)
Required dose less for electrons due to stronger elastic scatter (Henderson etc.)
Damage dose (in Gray) same for electrons and x-rays (ionization damage)
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
5nm
Brilot et al.
JSB (2012)
direct-e camera
5 frames/sec
Li et al.
Nat.Meth
10 (2013) 584
X-ray direct imaging: resolution restricted to
~ 20nm (zone plate)
Diffractive imaging capable of atomic resolution
but 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 study
Solid-state phase transitions
Metal-insulator transition
Nucleation and crystallization dynamics
Nanomechanical systems
Surface-charging effects
Plasmonics in nanostructures
Dynamics 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) 73
10fs, 70fs and 200fs pulses of 1.8keV (0.7nm) x-rays
focused to 7 microns (900 J/cm2, dose = 700MGy/pulse)  30MGy
give DPs of a membrane-protein complex (size ~ 10nm) damages
and demonstrate no damage below 70 fs (see below)
cooled
protein
Chapman et al. (2011)
Liquid-jet injector

and
pnCCD detectors (30Hz)
DP’s from detectors 
Photosystem-1
protein image 
reconstructed from
from 15,000 DPs
by coherent
diffractive imaging
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/2e0)(r/g2)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 collection
Slow down secondary processes e.g. by cooling specimen
The existence of these longer time scales
implies a dose-rate dependence of the damage dose Dc.
Dose-rate dependence of damage by x-rays
Warkentin et al.
Acta Cryst.(2013)
Change in damage dose reflects free-radical secondary damage
Evidence for dose-rate effects in electron-irradiation of organic materials
computer
simulation
+
+
Wery & Mansot, Microsc. Microanal. Microstruct.
4 (1993) 87. Formation of f.c.c. lead (detected in
diffraction pattern) in lead isooctanoate.
_
Egerton and Rauf, Ultramicroscopy
80 (1999) 247. Loss of O,C and N
from collodion at 90 K.
Simulation for 1nm electron probe (as in STEM):
dose De for
mass loss
from organic
polymer
at 90 K
Suggests that STEM can “outrun” mass loss (less damage in elemental map)
if probe current not high enough to cause appreciable temperature rise
Conclusions
Electrons and x-rays and electrons are both ionizing radiation
Radiation damage higher for EXELFS than for EXAFS
Damage may be less for elastic imaging by electrons
because 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 electrons
but 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 keV
If the signal is elastic, X-rays are 104 to 105 times more damaging
Protein/water contrast
0.4
10
X-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 = 2.6
but 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) / r(g/cm3)]
For 100keV electrons and typical organic material,
IMFP ~ 100 nm, Eav ~ 35 eV and r ~ 1.4 g/cm3,
giving 1 C/cm2  2500 MGy
or 1 electron/Angstrom2  4 MGy
Critical or characteristic dose Dc:
Amino acid (l-valine): 0.002 C/cm2 , 5 MGy
Chlorinated 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 structure
Diffusion from or into the irradiated area (composition change)
Escape of material form the specimen (mass loss)
Dielectric breakdown due to charge buildup
Disruption 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 effect
Fast XFEL pulses allow diffract & destroy (Chapman et al., 2011) positive
Diffusion allows recovery (Jiang & Spence, 2012) negative, threshold
Beam heating causes mechanical motion (Downing, 1987) negative
or 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 organics
So 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 not
magnetic attraction of parallel-trajectory electrons: Ftotal = (e/2e0)(r/g2)r
So 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 ( ~ 100mm in BNL apparatus, reduced by
focusing the laser illumination or using a small emitter tip)