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Surface ScienceWS 2019/20, L. Grill and G. Simpson
4. Microscopy
From Ancient Greek: μικρός (mikrós, “small”) + σκοπέω (skopéō, “I look at”)
What is microscopy?
A microscope is able to produce a magnified image of a small object
1 m
m
Epit
hel
ialc
ells
10
0 µ
m
1 µ
m
10
0 n
m
10
nm
1 n
m
0.1
nm
Red
cells
Bac
teri
a
Myc
op
lasm
a
Vir
use
s
Pro
tein
s
Am
ino
acid
s
Ato
ms
Radio Infrared Visible Ultraviolet γ- and x-rays
Op
tica
l m
icro
sco
pe
Hu
man
eye
Ele
ctro
nm
icro
sco
pe
10
µm
4. Microscopy
A170125.124200.dat
A170125.124200.dat Ch: 1
Biasvoltage: 0.03610V
Current: 3.4E-08A
Temperature: 0.00000 [K]
0 1 2 3 40
1
2
3
4
-0.005062 nm
-0.003062 nm
-0.001062 nm
0.0009381 nm
0.002938 nm
0.004938 nm
Epithelial cells Red cells Bacteria
Mycoplasma Virus Proteins
Amino acidsAtoms
Surface ScienceWS 2019/20, L. Grill and G. Simpson
4.1 Optical Microscopy
History
Earliest form of microscope – Eyeglasses
Salvino D'Armato degli Armati of Florence (died 1317) ??
«Qui diace Salvino d'Armato degl' Armati di Fir., Inventor degl'occhiali. Dio gli perdoni la peccata. Anno D. MCCCXVII»
“Here lies Salvino, son of Armato degli Armati of Florence, inventor of eyeglasses. May God forgive his sins. A.D. 1317”
The first type of „microscope“
What is generally meant as a microscope today is the compound microscope
• A device which uses two or more lenses to produce a magnified image of an object
The unaided human eye can distinguish two points 0.2 mm apart
Surface ScienceWS 2019/20, L. Grill and G. Simpson
Credit for the first microscope is usually given to Zacharias Jansen, in Middleburg, Holland, around the year 1595. Since Zacharias was very young at that time, it's possible that his father Hans made the first one, but young Zach took over the production
A replication microscope was made but the exact details and specificationsremain unknown
4.1 Optical Microscopy
History
Surface ScienceWS 2019/20, L. Grill and G. Simpson
Magnification
4.1 Optical Microscopy
Lens equation:
1
𝑓=
1
𝑑𝑜+
1
𝑑𝑖
Magnification equation:
𝑀 =ℎ𝑖ℎ𝑜
= −𝑑𝑖𝑑𝑜
Gives image distance and image height if the object distance, object height, and focal length are known
Equation can be derived from simple geometric arguments
Surface ScienceWS 2019/20, L. Grill and G. Simpson
Compound microscope
4.1 Optical Microscopy
• An object O is at distance a in front of objective
lens Lob
• Intermediate image O’ is projected
• O’ is further magnigifed by the eyepiece lens Ley
• Image O’’ is projected onto the retina
• The magnification is given by h‘/h
• Infinity space microscope has additional tube lens
• Creates a section into which accessories can be
added
• E.g. prisms, polarisers, retardation plates,
illuminators, etc
Compound microscope - two stage magnification• initial magnification with objective
• further magnification with eyepiece
Surface ScienceWS 2019/20, L. Grill and G. Simpson
Aberration
4.1 Optical Microscopy
The failure of rays to converge at one focus because of a defect in a lens or mirror
Spherical aberration
Perfect lens
Non-perfect lens
• Peripheral rays and axial rays have different focal points
• Image appears blurred as a result
• Affects the resolution of the microscope
Refracted to a greater degree
Refracted only slightly
Monochromatic light
Can be reduced by limiting exposure oflight to the centre of the lens or usingspecial lens grinding techniques,
Surface ScienceWS 2019/20, L. Grill and G. Simpson
Aberration
4.1 Optical Microscopy
The failure of rays to converge at one focus because of a defect in a lens or mirror
Chromatic aberration• The refractive index of materials varies with the
wavelength of light
• Known as dispersion:
• Image appears blurred as a result
• Affects the resolution of the microscope
white light
white lightdispersedlight
𝑣 =𝑐
𝑛
Blue light (low λ) refracted togreater extent than red (high λ)
Can be corrected by combiningmaterials of differing refractiveindex to bring different colours tofocus on same point
Surface ScienceWS 2019/20, L. Grill and G. Simpson
Image formation
4.1 Optical Microscopy
Diffraction is the speading of light that occurs when a beam of light interacts with an object
Huygens Principle: every point which a luminous disturbance reaches becomes a source of a spherical wave. The sum of the secondary waves determines the form of the wave.
If we have two elementary waves interacting witheach other, the result is interference of light.
Construcive interference produces points ofmaximum intensity
Destructive interference produces points ofminimum intensity
Surface ScienceWS 2019/20, L. Grill and G. Simpson
Image formation
4.1 Optical Microscopy
𝐼 𝛼 = 𝐼0𝑠𝑖𝑛
𝜋𝑎𝜆∙ sin 𝛼
𝜋𝑎𝜆∙ sin 𝛼
2
Intensity distribution given by:
tan𝛼 =𝑥
𝑑and sin 𝛼 =
𝑘𝜆
𝑎
An intensity minimum is given by:
tan𝛼 =𝑥
𝑑and sin 𝛼 =
(2𝑘+1)𝜆
2𝑎,
An intensity maximum is given by:
Of particular interest is the image of a point source of light. Images are madeup of myriad overlapping points of light.
The intensity distribution from single slit. Central maximum is 0th order, then 1st, 2nd, etc
Surface ScienceWS 2019/20, L. Grill and G. Simpson
Image formation
4.1 Optical Microscopy
Theory of image formation 1873 Ernst Abbe
Diffraction is the reason we see contrast in opticalmicroscopy (if light simply passed through thesample – no contrast)
Objects under microscope act like complexdiffraction gratings
Interference occurs in two places: diffraction plane and image plane
In image plane is collection of Airy circles (nextslide) which collectively make the image
At back focal plane is Fourier transform of image
Usually di is large, but not in microscope
1
𝑓=
1
𝑑𝑜+
1
𝑑𝑖
Surface ScienceWS 2019/20, L. Grill and G. Simpson
Image formation
4.1 Optical Microscopy
A point source of light consists of a central spot (Airy disk) surrounded by a series of diffraction rings
Central spot contains approx 84% of the light from thepoint source
Size of central disk is related to λ and the aperture angle ofthe lens
Radius of disk
Decreasing numerical aperture
𝑑 =1.22𝜆
2𝑁𝐴
Numerical aperture NA defineshow much light (brightness) andhow many diffraction orders arecaptured by the objective
Surface ScienceWS 2019/20, L. Grill and G. Simpson
Image formation
4.1 Optical Microscopy
Rayleigh criterion for spatial resolution:
a) Profile of single diffraction pattern
b) Profile of two disks separated by theRayleigh limit. Maximum overlapsfirst minimum. „Barely resolved“.
c) Maximum overlaps with secondminimum. „Clearly resolved“
Obtaining an image whose resolution is limited by the size of the diffraction spot is said to bediffraction limited
Resolution limit with good optics and high NA is approximately 250 nm
Surface ScienceWS 2019/20, L. Grill and G. Simpson
Breaking the diffraction limit
4.2 Super Resolution Microscopy
As we have seen, the wave nature of light limits reolution of conventional microscopes toapproximately half of the wavelength of light used.
Many sub-diffraction limit techniques rely on flourescence methods
Eric Betzig Stefan W. Hell William E. Moerner
The Nobel Prize in Chemistry 2014 was awarded "for the development of super-resolved fluorescence microscopy".
Surface ScienceWS 2019/20, L. Grill and G. Simpson
Breaking the diffraction limit
4.2 Super Resolution Microscopy
As we have seen, the wave nature of light limits reolution of conventional microscopes toapproximately half of the wavelength of light used.
Many sub-diffraction limit techniques rely on flourescence methods
Jablonski Diagram
Shows energy levels occupied by an excited electronwithin a fluorescent molecule. (Chlorophyll a)
Absorption of a photon causes excitation fromground electronic state to higher excited state.
Collapse back to ground state can occur though:
Internal conversionFluorescencePhosphorescence
Blue photon
Red photon
Surface ScienceWS 2019/20, L. Grill and G. Simpson
Breaking the diffraction limit
4.2 Super Resolution Microscopy
Fluorophores
Fluorescein
Chlorophyll a
Green Fluorescent Protein (GFP)
Pulmonary artery epithelial cellsshowing photobleaching
Excitation Emission
Surface ScienceWS 2019/20, L. Grill and G. Simpson
STimulated Emission Depletion fluorescence microscopy (STED)
4.2 Super Resolution Microscopy
S0 – ground electronic stateS1 – 1st excited electronic stateL – Vibrational levels
The excitation is achieved by a laser focussed trough a pinhole andan objective lens
The sample contains a fluorophore
The laser light is scanned over the sample
The size of the laser spot is again limited by diffraction so, ifunmodified, the resolution will not be increased.
Surface ScienceWS 2019/20, L. Grill and G. Simpson
STimulated Emission Depletion fluorescence microscopy (STED)
4.2 Super Resolution Microscopy
In order to reduce the area of each fluorescent point stimulated emission is employed
Point spread function (PSF):
Describes the profile of the excitationlight
J1 – first order Bessel functionν - 2πrNA/λexc
r – distance from focal pointNA - Numerical apertureλexc – excitation wavelength
In order to reduce the spatial extent of hexc(ν), thefluorescence is inhibited in the outer regions
For this, an additional beam of light is used – theSTED beam
Surface ScienceWS 2019/20, L. Grill and G. Simpson
STimulated Emission Depletion fluorescence microscopy (STED)
4.2 Super Resolution Microscopy
Excitation photon promotes electron from singlet S1 groundstate to the some vibrational level in the first excited state S1
Excitation quickly followed by internal conversion to lowestexcited vibrational state (picoseconds).
The fluorescence occurs as the electron relaxes back to theground state
However:If an additional photon comes in with energy equal totransition from S1 to a vibrational state of S0 we getstimulated emission
Result is two photon with same properties (phase, polarisation, etc)
Importantly, the simulated emission photons have different energy (wavelength) to the fluorescence photons
This means they can be filtered out easily.
Excitation laser STED laser
Signal
Surface ScienceWS 2019/20, L. Grill and G. Simpson
STimulated Emission Depletion fluorescence microscopy (STED)
4.2 Super Resolution Microscopy
The STED beam is donut shaped andsuperimposed on the excitation beam
The resulting PSF of the fluorescencesignal is reduced
The combined laser light is scanned over thesurface to reveal sub-diffraction-limit features
Surface ScienceWS 2019/20, L. Grill and G. Simpson
STimulated Emission Depletion fluorescence microscopy (STED)
4.2 Super Resolution Microscopy
Octametic arrangement of peripheraltransmembrane GP210 protein aroundcore protein in a nuclear pore complexin immunolabeled Xenopus cells
Brings resolution to the order of50 nm
J. Biomed. Opt. 19(8), 080901
Surface ScienceWS 2019/20, L. Grill and G. Simpson
Single molecule imaging techniques
4.2 Super Resolution Microscopy
Another method to circumvent Abbe limit: single molecule emitters
Causing fluorescence from single, well-separated molecules allows individual molecules to be located
EYFP fluorescent protein anchored to ParA protein in bacterial cell
Surface ScienceWS 2019/20, L. Grill and G. Simpson
4.3 Electron microscopy
Ernst Ruska Gerd Binnig Heinrich Rohrer
The Nobel Prize in Physics 1986 was divided, one half awarded to Ernst Ruska "for his fundamental work in electron optics, and for the design of the first electron microscope", the other half jointly to Gerd Binnig and Heinrich Rohrer "for their design of the scanning tunneling microscope"
First prototype electron microscope from Ernst Ruska 1933
Surface ScienceWS 2019/20, L. Grill and G. Simpson
4.3 Electron microscopy
Why electrons?
Resolution is limited by the wavelength of the illuminating radiation
Electrons are particles with negative charge and mass 1/1836 that of a proton
Wave-particle dualism postulated by de Broglie (Nobel Prize 1929)
Electrons have wave nature and their wavelength is directly related to theirmomentum:
𝜆 =ℎ
𝑝=
ℎ
𝑚𝑣
λ - Wavelengthp - Momentumm - Massv – Velocityh – Plank constant
By controlling the energy and hence speed of the electrons we can choosethe wavelength
Electron microscopy can provide resolution down to 0.5 nm (atomic scale)
Surface ScienceWS 2019/20, L. Grill and G. Simpson
4.3 Electron microscopy
Electron generation
A low votage is applied tocathode filament (W or LaB6)
Through resistive heatingelectrons gain sufficientkinetic enery to escape fromits surface
Free electron in vacuum arepulled away from the hotsurface by placing the positive anode nearby
High voltage between anode and cathode accelerates electrons towards anode
Hole in anode allows a beam of electrons trough
Electrons continue unhindered through the vacuum
Wehnelt cylinder pre-focuses the electrons before acceleration towards to anode to increase intensity
Surface ScienceWS 2019/20, L. Grill and G. Simpson
4.3 Electron microscopy
Types of electron interaction
How can the electrons interact with the sample?
Surface ScienceWS 2019/20, L. Grill and G. Simpson
4.3 Electron microscopy
Types of electron interaction
Elastic scattering
No energy is tranferred from the electronto the sample
Backscattered electrons are also elasticallyscattered
Due to electron being deflected in somedirection by interaction with the Coulomb potential of the atom
Surface ScienceWS 2019/20, L. Grill and G. Simpson
4.3 Electron microscopy
Types of electron interaction
Inelastic scattering
Energy is transferred between the electronsand the sample
Information rich, many different signals:
X-RaysAuger electronsSecondary electronsPlasmonsPhonons
Surface ScienceWS 2019/20, L. Grill and G. Simpson
4.3 Electron microscopy
TEM
Surface ScienceWS 2019/20, L. Grill and G. Simpson
4.3 Electron microscopy
Electromagnetic lens
𝑭 = −𝑒 𝑬 + 𝒗 × 𝑩
𝑭 = 𝑒𝑣𝐵sin(𝒗, 𝑩)
E: electric field strengthB: magnetic field stregthe/v: charge/velocity of electrons
Magnetic lens is a copper coil inside iron pole pieces
Passing current through the wires creates a magnetic field
Field is strong at edges and weak in the centre
Electrons experience the Lorenz force F:
Electrons are deflected strongly/weakly at edges/centre
Incoming parallel beam of electrons is focussed
By adjusting the current in the copper wire the B fieldstrength can be adjusted
Focusing effect can therefore be controlled
Surface ScienceWS 2019/20, L. Grill and G. Simpson
4.3 Electron microscopy
Transmission electron microscopy (TEM)
A beam of electrons is produced in the electron gun
Focused through lenses
Transmitted through an ultra thin specimen
Magnified by further lenses
Detected by a phosphorescent screen or a CCD
Sample preparation is key.
Sample thickness vaires between 10 and 500 nm depending on the material
TEM grid
Microtomy
Solution dispersion
Focusedion beam (FIB)
Surface ScienceWS 2019/20, L. Grill and G. Simpson
4.3 Electron microscopy
Transmission electron microscopy (TEM)
Most common imaging technique is Bright Field
• Contrast is formed directly by diffraction and absorption of electronsby the sample (like optical microscopy)
• Simple 2D projection of the sample• Dark areas represent areas of higher electron scattering (denser or
higher atomic number)• Light areas are where electrons pass through the sample more easily• Similar to Lamber-Beer
Rat‘s liver 1 µm scale bar
Bright field anddark field image ofeutectic alloy(AlSi12(Mg))
Dark field imagehighlights Mg2Si precipitates
In Dark Field imaging, illuminationis tilted to select a specificdiffracted beam
Used to image a subset of thesample which satisifes the Bragg condition
Surface ScienceWS 2019/20, L. Grill and G. Simpson
4.3 Electron microscopy
High resolution TEM
Atomic resolution TEM image of a triple and a quadruple line at the interface between Σ3 boundaries and a Σ9 boundary in nanocrystalline palladium. H. Rösner and C. Kübel et al., Acta Mat., 2011, 59, 7380-7387
Very thin slice of crystal tilted so that lowindex direction is perpendicular to electronbeam
The electron wave interacts with theperiodic crystal structure.
Driffraction of electron beam due to Bragg condition
Interference of electron waves
Contrast mechanism difficult to interpret
2𝑑sin𝜃 = 𝑛𝜆
Surface ScienceWS 2019/20, L. Grill and G. Simpson
4.3 Electron microscopy
Scanning Electron Microscopy (SEM)
Surface ScienceWS 2019/20, L. Grill and G. Simpson
4.3 Electron microscopy
Scanning Electron Microscopy (SEM)
Electron beam is highly focused to a tiny spot and scanned pixel by pixel over a surface
At each pixel secondary electrons (SE) are generated
The SE are detected then amplified.
Signal is fed to a computer and image is displayed
SE (<50 eV) can only escape from a smallvolume (surface sensitve)
Backscattered electrons (BSE) have higherenergy and can therefore escape from deeper
"universal curve„Mean free path of SE
Surface ScienceWS 2019/20, L. Grill and G. Simpson
4.3 Electron microscopy
Imaging using SE
SE escape depth independent of PE energy
Intensity is increased with lower PE energy (i.e. higherPE energy causes more SE to be produced deeper andcannot escape)
Intensity of SE escaping from surface at each pixelrepresents contrast
Contrast a function of angle of PE and specimen(depth of field)
Escape depth aslo dependent on atomic number:10-100nm Carbon2-3nm Chromium1-2nm Platinum
Biological samples are coated with thin layer of Pt or Au
Electrical grounding (conducting samples) important to stop charging of sample
Surface ScienceWS 2019/20, L. Grill and G. Simpson
4.3 Electron microscopy
Imaging using SE
Surface ScienceWS 2019/20, L. Grill and G. Simpson
4.3 Electron microscopy
Imaging using BSE
Backscattered electrons can reveal differences in composition (heavy elements backscatter morestrongly than light elements)
BSE must be detected close to the objective lens
Red blood cell showing location of surface protein antibodiesaggregated with gold particles
Surface ScienceWS 2019/20, L. Grill and G. Simpson
4.3 Electron microscopy
Electron detection
SE collected by a grid with +200 – 500 V applied to it.
SE hit a scintillator which coverts electrons tophotons
Photons guided towards photomultiplier tube
Photoelectrons are amplified to produce a measurable current
Current is the signal
Surface ScienceWS 2019/20, L. Grill and G. Simpson
4.4 Scanning Tunnelling Microscopy
History
The Nobel Prize in Physics 1986
Gerd Binnig Heinrich Rohrer
IBM Zurich
STM is the first member in the larger ‘family’ of instruments known as Scanning Probe Microscopes
Use a sharp probe which is brought into close proximity with a surface.
Distance so small that a measurable tunnel current is present
Tip is raster scanned over the surface while measuring current/height.
Atomic scale features can be resolved
Surface ScienceWS 2019/20, L. Grill and G. Simpson
4.4 Scanning Tunnelling Microscopy
Overview of STM set-up
1 Metallic tip2 Piezoelectric scanner3 Current amplifier4 Feedback loop
The metallic tip is brought to within a few Ångströms of the conductingbiased surface using the coarse positioning system. Tunnel current isdetected and amplified. Feedback system maintains constant current byadjusting the height of the tip as it is scanned over the surface.
Surface ScienceWS 2019/20, L. Grill and G. Simpson
A particle with energy E encounters a potential energy barrier of height V
Classical case: A golf ball with kinetic energy reaches a hill. Not enough energy to overcome barrier. Ball rolls back down the hill (reflected)
Quantum case: Electron approaches potential barrier (vacuum). Barrier height exceeds electron energy. Electron is described by wavefunction. Wavefunction decay exponentially in the barrier.If barrier is thin enough probability density is non-zero at other side.
4.4 Scanning Tunnelling Microscopy
Tunnelling
Surface ScienceWS 2019/20, L. Grill and G. Simpson
4.4 Scanning Tunnelling Microscopy
Tunnelling
−ℏ2
2𝑚𝜵2 + 𝑉 𝒓 Ψ 𝒓 = 𝐸Ψ(𝒓)Time-independent Schrödinger Equation
Hamiltonian operator(total energy: kinetic+potential)
Wavefunction
Energy eigenvalues
Wavefunction:
Complex mathematical functionContains all measurable information about systemΨ*Ψ represents probability density (summed over all space = 1)For a free particle Ψ is a sine wave (SE exactly solvable)
Surface ScienceWS 2019/20, L. Grill and G. Simpson
4.4 Scanning Tunnelling Microscopy
Tunnelling
Particle reaches potential barrier
Wavefunction related toprobability of finding particle
Transmission probability isrelated to ratio of amplitude in c compared to a
A measure of the current
Probability decays exponentiallyin gap b
Local density of states (LDOS)
I depends exponentially on d!Also dependent on V and φ
𝐼 𝑑 = 𝐴𝑉𝑒−2𝜅𝑑 𝜅 =2𝑚𝜙
ℏ
Surface ScienceWS 2019/20, L. Grill and G. Simpson
4.4 Scanning Tunnelling Microscopy
Tunnelling
Metal: Electrons fill states upto the Fermi energy, EF. The work function Φ describesthe energy an electron at EF
needs in order to leave themetal
In the case of STM, the tip isbrought close to the sample. The wavefunction of theelectrons in the tip andsample overlap. Tunnellingdoes not occur at zero biasdue to absence of availablestates.
Applying a –ve bias tosample fills states in sample. Electrons in filled statestunnel thought the barrier toempty states of the tip. A net tunnel current ismeasured.
The measured current at the tip position is a measure of the local density of states (LDOS)
Surface ScienceWS 2019/20, L. Grill and G. Simpson
4.4 Scanning Tunnelling Microscopy
Tunnelling
The exponential relation leads to extreme sensitivity tochanges in the distance between the STM tip and the surface.
Back of envelope calculation:
Typical work function value for metal: 4 eVTypical atomic diameter: 3 Å
Change in d of this distance corresponds to factor1000 change in It.
High sensitivity to d means STM signal isdominated by the last atom of the tip.
𝐼 𝑑 = 𝐴𝑉𝑒−2𝜅𝑑 𝜅 =2𝑚𝜙
ℏ
Surface ScienceWS 2019/20, L. Grill and G. Simpson
4.4 Scanning Tunnelling Microscopy
Scanning
Signal measured is dominated by last atom of tip.
The tip is scanned over the surface to produce an STM image
In order to resolve atomic scale features of the surface it isimportant to be able to move the STM tip with subangstrom resolution.
Sub-Ångström control is achieved using piezoelectricelements.
Piezoelectric effect: reversible change in physicaldimensions of a meterial in response to an externallyapplied electric field.
Δ𝑙 = 𝑐𝑙
ℎ𝑈
lΔl – change in lengthc – piezoelectric coefficientl – lengthh – wall thiknessU – applied voltage
Typical resolution: 0.1 Å laterally; 0.01 Å vertically
Surface ScienceWS 2019/20, L. Grill and G. Simpson
4.4 Scanning Tunnelling Microscopy
Two main modes of scanning
Constant Current• A tunnel current is set• Tip moves over features of surface• Feedback loop responds quickly to
adjust the height of the tip• Tunnel current is maintained at
same value• Height of tip gives signal• Most common
Constant Height• Only x,y piezos used to scan• Z-position of tip is unchanged• Due to corrugation of surface,
tunnel gap changes• Leads to variation in current• Current gives signal• Can lead to tip crashes
https://www.youtube.com/watch?v=LDKnhfdBj3Y
Surface ScienceWS 2019/20, L. Grill and G. Simpson
4.4 Scanning Tunnelling Microscopy
Tip preparation
Electrochemical etching
Chemical reaction at the tip slowly depletes the metal of the tipTypically tungstenOften covered in layer of insulating oxide! Cleaning required
Surface ScienceWS 2019/20, L. Grill and G. Simpson
4.4 Scanning Tunnelling Microscopy
Tip preparation
Wire cutting
Much more simple, brutal methodWire (Pt80/Ir20) is stretched and cut with sharp tool
Leads to much poorer definition of apex
For most purposes irrelevant as the STM signal isdependent only on the last atom
Surface ScienceWS 2019/20, L. Grill and G. Simpson
4.4 Scanning Tunnelling Microscopy
Tip preparation
In situ tip forming is done toimprove the tip apex
STM tip is crashed into themetal surface
Slowly drawn out
In best case resulting in single atom apex
As tip is drawn out of surfacequantised level in theconductance can be seen
Aspect ratio of tip can beimportant for getting a sharp image.
Surface ScienceWS 2019/20, L. Grill and G. Simpson
4.4 Scanning Tunnelling Microscopy
Example images
Constant current STM image of Au(111) surfaceshowing step edge, herringbone reconstruction, and atomic resolution
Typical „multi-tip“ STM image
Si(111)-(7x7) reconstruction
Surface ScienceWS 2019/20, L. Grill and G. Simpson
4.4 Scanning Tunnelling Microscopy
Sample preparation - sputtering
Sputter yield – number of surfaceatoms ejected per incoming ion
On silicon
High energy ions impact a surface.
Series of collisions occurs in the top layers of atoms
Can lead to many processes(embedding, adsorption, disclocations, e- and M+ ejection)
Surface ScienceWS 2019/20, L. Grill and G. Simpson
4.4 Scanning Tunnelling Microscopy
Sample preparation - sputtering
Au(111) surface after sputtering at 400 K with 1 keV Ne+ ions
Aprroximately 10 layers removed
Surface ScienceWS 2019/20, L. Grill and G. Simpson
4.4 Scanning Tunnelling Microscopy
Sample preparation - Annealing
After sputtering where the top layers of the surface are removed, the surface is heated to inducethermal healing.
This induces mass transport on the surface (diffusion of atoms)
In order to acheive lowest energy large flat terraces are formed
Above: Ag(001) surface after sputtering at 180 K, 380 K, and 450 K (1 keV Ne+, 1200 s)
Surface ScienceWS 2019/20, L. Grill and G. Simpson
4.4 Scanning Tunnelling Microscopy
Sample preparation – Molecular deposition
Sublimation from filament heated crucible:
1. Electrical contacts for heating filament2. Thermocouple contacts3. CF flange for attachement to UHV system4. Molecules to be sublimed5. Glass tube with filament wrapped around it.
Low T
High T
Surface ScienceWS 2019/20, L. Grill and G. Simpson
4.4 Scanning Tunnelling Microscopy
Sample preparation – Molecular deposition
Electrospray from solvent
1. Molecules or nanoparticles dissolved/suspended in solution2. Solution injected from fine capillary3. High voltage applied to accellerate4. Uniform solvated droplets formed5. Differential pumping stages leads to evaporation of solvent6. Intact molecule/nanoparticles arrive at surface and adsorb Electrospray deposited unfolded CytC in
different charge states
Surface ScienceWS 2019/20, L. Grill and G. Simpson
4.4 Scanning Tunnelling Microscopy
Atomic/molecular manipulation
STM not only useful for imaging structures at the atomic scale. The STM tip can be used to maniulatesingle atoms/molecules
Surface ScienceWS 2019/20, L. Grill and G. Simpson
4.4 Scanning Tunnelling Microscopy
Atomic/molecular manipulation
Van der Waals, chemical forces, or Pauli repulsion between tip and adsorbate.
Pulling (attractive),
Pushing (repulsive),
Sliding
https://www.youtube.com/watch?v=oSCX78-8-q0
Eigler, D. M. & Schweizer, E. K. Nature 344, 524–526 (1990)
Surface ScienceWS 2019/20, L. Grill and G. Simpson
4.4 Scanning Tunnelling Microscopy
Atomic/molecular manipulation
Tunnelling electrons can inelastically interact with molecules to cause chemical reactions on surfaces
Cis-/trans- isomerisation of azobenzeneDissociation of oxygen molecules
Phys. Rev. Lett. 78, 4410-4413 (1997)
Surface ScienceWS 2019/20, L. Grill and G. Simpson
4.4 Scanning Tunnelling Microscopy
Atomic/molecular manipulation
Bias between tip and sample means that a local electric field is present. Can be used to manipulatemolecules
Increasing d in the limit ofzero tunnel current
A161005.152354.dat
A161005.152354.dat Ch: 1
Biasvoltage: 1.03510V
Current: 2.7E-13A
Temperature: 0.00000 [K]
0 1 2 3 40
1
2
3
4
-0.1124 nm
-0.06237 nm
-0.01237 nm
0.03763 nm
0.08763 nm
Rotation of dipolar nanocar
Surface ScienceWS 2019/20, L. Grill and G. Simpson
4.4 Scanning Tunnelling Microscopy
Atomic/molecular manipulation
Bias between tip and sample means that a local electric field is present. Can be used to manipulatemolecules
Increasing d in the limit ofzero tunnel current
A161005.152141.dat
A161005.152141.dat Ch: 1
Biasvoltage: 1.03510V
Current: 2.7E-13A
Temperature: 0.00000 [K]
0 1 2 3 40
1
2
3
4
-0.1124 nm
-0.06237 nm
-0.01237 nm
0.03763 nm
0.08763 nm
Surface ScienceWS 2019/20, L. Grill and G. Simpson
4.4 Scanning Tunnelling Microscopy
Atomic/molecular manipulation
Bias between tip and sample means that a local electric field is present. Can be used to manipulatemolecules
Increasing d in the limit ofzero tunnel current
A161005.151944.dat
A161005.151944.dat Ch: 1
Biasvoltage: 1.03510V
Current: 2.7E-13A
Temperature: 0.00000 [K]
0 1 2 3 40
1
2
3
4
-0.1124 nm
-0.06237 nm
-0.01237 nm
0.03763 nm
0.08763 nm
Surface ScienceWS 2019/20, L. Grill and G. Simpson
4.4 Scanning Tunnelling Microscopy
Atomic/molecular manipulation
Bias between tip and sample means that a local electric field is present. Can be used to manipulatemolecules
Increasing d in the limit ofzero tunnel current
A161005.151756.dat
A161005.151756.dat Ch: 1
Biasvoltage: 1.03510V
Current: 2.7E-13A
Temperature: 0.00000 [K]
0 1 2 3 40
1
2
3
4
-0.1124 nm
-0.06237 nm
-0.01237 nm
0.03763 nm
0.08763 nm
Surface ScienceWS 2019/20, L. Grill and G. Simpson
4.4 Scanning Tunnelling Microscopy
Atomic/molecular manipulation
Bias between tip and sample means that a local electric field is present. Can be used to manipulatemolecules
Increasing d in the limit ofzero tunnel current
A161005.150850.dat
A161005.150850.dat Ch: 1
Biasvoltage: 1.03510V
Current: 2.7E-13A
Temperature: 0.00000 [K]
0 1 2 3 40
1
2
3
4
-0.1124 nm
-0.06237 nm
-0.01237 nm
0.03763 nm
0.08763 nm
Surface ScienceWS 2019/20, L. Grill and G. Simpson
4.4 Scanning Tunnelling Microscopy
Atomic/molecular manipulation
Bias between tip and sample means that a local electric field is present. Can be used to manipulatemolecules
Increasing d in the limit ofzero tunnel current
A161005.150651.dat
A161005.150651.dat Ch: 1
Biasvoltage: 1.03510V
Current: 2.7E-13A
Temperature: 0.00000 [K]
0 1 2 3 40
1
2
3
4
-0.1124 nm
-0.06237 nm
-0.01237 nm
0.03763 nm
0.08763 nm
Surface ScienceWS 2019/20, L. Grill and G. Simpson
4.4 Scanning Tunnelling Microscopy
Scanning tunnelling spectroscopy
We know that the tunnel current in STM is a function of the local density of states of both thesample and the tip:
𝐼 ∝ න0
𝑒𝑉
𝜌𝑠 𝐸𝐹 − 𝑒𝑉 + 𝜖 𝜌𝑇 𝐸𝐹 + 𝜖 𝑑𝜖
𝑑𝐼
𝑑𝑉∝ 𝜌𝑠 𝐸𝐹 − 𝑒𝑉
surface tip
We are generally interested in the states of the surface only. However, above equation implies a convolution between surface and tip states. Further, tunelling transmission probability (not shownabove) depends in unknown manner on V.
Approximation: Assume that transmission probabiliy is constant; assume a smooth density ofstates of tip.
Integrated density of states
Density of states
Surface ScienceWS 2019/20, L. Grill and G. Simpson
4.4 Scanning Tunnelling Microscopy
Scanning tunnelling spectroscopySpectrum is acquired by ramping the biasand measuring the tunnel current
Feedback control is deactivated
Changes in the LDOS of the surface leadto features in I/V curve
More useful to inspect the differential conductance dI/dV and function of V
Corresponds to LDOS of sample (approximately – care must be takenupon interpretation)
Polarity of bias allows access tooccupied/unoccupied states
dI/dV can be obtained by numericaldifferentiation of I/V or by lock-in techniques.
Surface ScienceWS 2019/20, L. Grill and G. Simpson
4.4 Scanning Tunnelling Microscopy
Scanning tunnelling spectroscopy
Filled state (negative bias) andempty state (positive bias) images of Si(001)-(2x1) andmodel depicting shape of π andπ* orbitals
dI/dV spectra of the Si(111)-(7x7) surface.Differences observed when tunnel gap is changedShows that spectra affected by charge transportbetween surface and sample holder.
Physical review. B, Condensed matter 80(12)
Surface ScienceWS 2019/20, L. Grill and G. Simpson
4.4 Scanning Tunnelling Microscopy
Scanning tunnelling spectroscopy
STS can also be used to investigate theelectronic structure of molecules
Adsorption on NaCl bilayer decouples themolecule from the metallic surface
dI/dV spectrum then shows clearly theHOMO and LUMO
Resonant tunnelling at these resonancesallows one to image the MOs.
Science Vol. 317, Issue 5842, pp. 1203-1206
Surface ScienceWS 2019/20, L. Grill and G. Simpson
4.4 Scanning Tunnelling Microscopy
Scanning tunnelling spectroscopy
Further example of molecular orbital imaging – high temporal resolution.
Teraherz waveform excites only the HOMO and opens transient tunnel channel. Single electronsremoved from this molecular orbital and detected as shift in tunnel current.
Result is 100 fs snapshot of HOMO
Nature 539, 263 (2016)
Surface ScienceWS 2019/20, L. Grill and G. Simpson
4.4 Scanning Tunnelling Microscopy
Scanning tunnelling spectroscopy
Removal of electron from HOMO causes vertical vibration of molecule. Second time-delayed pulse canmeasure instantaneous height of molecule.
Nature 539, 263 (2016)
Surface ScienceWS 2019/20, L. Grill and G. Simpson
4.4 Scanning Tunnelling Microscopy
Scanning tunnelling spectroscopy
Also possible to access informationabout vibrational modes of adsorbedmolecules.
Inelastic tunnelling of electrons canexcite vibrational levels
Provides a small (~1%) increase in tunnelling current due to extra channel opening up
The second derivative shows peaks in the position corresponding to theenergy of the vibrations.
Requires high-stability and lowtemperature to ensure moleculesoccupy vibrational ground state
Surface ScienceWS 2019/20, L. Grill and G. Simpson
Science 280, 1732
4.4 Scanning Tunnelling Microscopy
Scanning tunnelling spectroscopy
Vibrational modes of single adsorbed ethene molecule on Cu(100)
Surface ScienceWS 2019/20, L. Grill and G. Simpson
4.4 Scanning Tunnelling Microscopy
Scanning tunnelling spectroscopy
Surface ScienceWS 2019/20, L. Grill and G. Simpson
4.4 Scanning Tunnelling Microscopy
Single molecule switching
Intramolecular hydrogen tautomerisation reaction observed in naphthalocyanine
Charge redistribution upon proton transfer leads to apparent rotation of LUMO
Changes are detected in tunnel current Science Vol. 317, Issue 5842, pp. 1203-1206
Surface ScienceWS 2019/20, L. Grill and G. Simpson
4.4 Scanning Tunnelling Microscopy
Single molecule chemistry
Tip-induced formation of biphenyl from iodobenzene on Cu(111)
Phys. Rev. Lett. 85, 2777
Surface ScienceWS 2019/20, L. Grill and G. Simpson
4.4 Scanning Tunnelling Microscopy
Single molecule chemistry
Thermally induced heirarchical growthof ordered 1D and 2D networks on Au(111)
Nature Chemistry 4, 215–220 (2012)
Surface ScienceWS 2019/20, L. Grill and G. Simpson
4.5 Atomic Force Microscopy
AFM
A sharp tip is mounted on the end of a cantilever.Depending on the mode of operation, the cantilever can be oscillated using the piezo driver.The force of attraction/repulsion between surface and tip modifies deflection of the cantilever or theoscillation frequency.This deflection is recorded by a photodetectorX,Y,Z piezos allow the tip to be scanned relative to the surface
Surface ScienceWS 2019/20, L. Grill and G. Simpson
4.5 Atomic Force Microscopy
Lennard Jones potential
Repulsive: Very small tip-sample distances
Exchange interactions due to overlapof electronic orbitals (Pauli repulsion)
Attractive:Instantaneous polarisation of atomsinduces polarisation of nearby atoms(van der Waals)
Other attractive forces can play large role (electrostatic – H-bonding, dipoleinteraction)
Results in attractive interaction
Surface ScienceWS 2019/20, L. Grill and G. Simpson
4.5 Atomic Force Microscopy
Contact Mode AFM
Replusive forces
Tip is in contact with the surface
The tip follows the topography of thesurface
As topography changes, the cantilever isdeflected
High resolution on hard surfaces (eg, metals)
Soft samples can be deformed due to high forces
Surface ScienceWS 2019/20, L. Grill and G. Simpson
4.5 Atomic Force Microscopy
Non-conact Mode AFM
Attractive forces
Tip is not in contact with the surface
The cantilever is oscillated above thesample
Two modes: frequency modulation, amplitude modulation
Frequeny modulation – feedback loopused to regulate amplitude and change in frequency of cantilever due to attractiveforces is measured
Amplitude modulation - Cantilever isdriven with a set frequency and theamplitude is measured.
Useful for biological samples
Surface ScienceWS 2019/20, L. Grill and G. Simpson
4.5 Atomic Force Microscopy
Tapping Mode AFM
Amplitude of oscillations is measured astip scans over the surface
Less destructive than contact mode
The tip only contacts the surface at a seriesof points over the surface
No dragging or tip-wear
Surface ScienceWS 2019/20, L. Grill and G. Simpson
4.5 Atomic Force Microscopy
Amplitude modulation
Sensor is excited at Fdrive, just off ofresonance frequency.
As tip scans over surface, resonancefrequecy changes depending on forcesbetween sample and tip.
Chance in amplitude of oscillation givesa measure of force.
Can be operated both with feedback control (tip height is adjusted in order to maintain A = Aset)Or in constant height mode.
Major disadvantage: in vacuum scan speed is very low due to use of high quality factor (Q) sensors and the long time for the oscillation to reach steady state after a change in Fres
-rather used in air or liquid
Surface ScienceWS 2019/20, L. Grill and G. Simpson
4.5 Atomic Force Microscopy
Frequency modulation
Damped oscillator:
The cantilever is driven with frequency ω
Energy exchange is maximised when drivingsignal has phase difference of 90°
Signal collected from deflection of cantileverand signal is adjusted to maintain oscillation ofcantilever at resonance
Surface ScienceWS 2019/20, L. Grill and G. Simpson
4.5 Atomic Force Microscopy
qPlus sensor Quartz tuning fork with immobilised upperprong.
Metal tip attached to lower prong
𝐹 = 𝑘𝑥
Hooke‘s lawF – forceK – spring constantX - displacement
Conventional cantilever has typical k = 10 N/m
To prevent „snap-to-contact“ restoring force must belarger than 100 nN
For cantilever – 10nm oscillation aplitude
k for qPlus is 1000- 10000 N/m – very stifftherefore very low aplitude oscillation
Surface ScienceWS 2019/20, L. Grill and G. Simpson
4.5 Atomic Force Microscopy
qPlus sensor
Surface ScienceWS 2019/20, L. Grill and G. Simpson
4.5 Atomic Force Microscopy
Kolibri sensor
Surface ScienceWS 2019/20, L. Grill and G. Simpson
4.5 Atomic Force Microscopy
Sub-molecular resolution
Pentacene on Cu(111) imaged both with STM and AFM with CO functionalised tip
AFM images using different tip modifications
A Ag tip;B CO tipC Cl tipD pentacene tip
CO tip gives tures image of molecular structure
Surface ScienceWS 2019/20, L. Grill and G. Simpson
4.5 Atomic Force Microscopy
Sub-molecular resolution
The contrast depends stronglyon the tip-sample distance andhence the magnitude of theforces acting on the tip.
Featureless depression at high distance (attractive interaction) – van der Waals background
At very small tip-sample distances Pauli repulstionbecomes dominant
Areas of high electron density(i.e. chemical bonds) showhigher force than in the middleof carbon rings
Leads to bond imaging
Surface ScienceWS 2019/20, L. Grill and G. Simpson
4.5 Atomic Force Microscopy
Sub-molecular resolution
Bond length and hence bond ordercan be qualitatively measured usingCO-tip NC-AFM
Surface ScienceWS 2019/20, L. Grill and G. Simpson
4.5 Atomic Force Microscopy
CO tip
2 CO molecules on Cu(111) surface
Picked up by retracting 0.3 Å and applying 2.5 V until sudden change in tunnel current is seen
Reimaging shows one CO has been picked up
Modified tip gives different contrast of remaining CO molecule
Surface ScienceWS 2019/20, L. Grill and G. Simpson