Textbook: pages 23-37

Atomic models
Structure of matter, matter waves, atomic and
molecular interactions. Atomic force microscopy.

Balázs Kiss
[email protected]

Nanobiotechnology and Single Molecule Research Group, • Democritus (~400 BC): proposition of atomic structure („atomos”: indivisible)

Department of Biophysics and Radiation Biology, • Dalton (1803): stoichiometric law: elements consist of identical constituents
Semmelweis University • Thomson (1897): discovery of electron (cathode rays)

• Rutherford (1909-1911): nucleus (nucleons: p+ and n0) and electrons

2. October 2019.
• Bohr (1913): discrete energy states
2

How are stable structures created/formed? Fundamental interactions in physics

Interaction type Binding particle Range (m) Relative strength

10-40
gravitation every particle infinite (~1/r2)

electromagnetic
165 000 000 000 x
charged particles infinite (~1/r2) 10-2
(Coulomb)
strong nuclear nucleons 10-15 1
weak nuclear every particle 10-18 10-13

Coulomb-interaction Gravitation
?
repulsion attraction
mB
QB
macroscopic scale: Atomium nanoworld: face-centered cubic lattice of Fe F F
F F
Governing principle: QA
mA r
r attraction

consequence: repulsive attractive consequence:

DISORDER interaction interaction ORDER
QA  QB m A  mB
FC  k  Fg  G 
3 r2 r2 4

Electric potential energy (Epot) Structure of the Atom

nucleus, including: Z: atomic number
F1…Fn W  F  s  F  Δr (number of protons)
• protons (p+)
QB QA QA nucleons
F ? • neutrons (n0) N: neutron number
Qtotal,nucl  Z  e A: mass number
r changes continuously!
(=Z+N)
positive charge (fixed) How much energy is needed to separate the - charge?
K L M shells
Epot
nucleus

repulsion electrons e-
Electric
Qtotal,e    Z  e
potential energy: d~0.1 nm

E pot  W r
W
QA  QB 1 2
k
QA  QB Etotal < 0: bound electron
E pot  k  Ekin
2
mv Epot
r
r attraction Etotal > 0: free electron
the negative (integral calculation)
charge is
Q A  QB Etotal  E pot  Ekin
transported into Wr    k 
infinite r 5 6

1
 The energy states of the electron Particle-wave duality of the electron
cf. particle-wave duality of the photon

e-beam is bent due to

l: azimuthal quantum number the presence of the
magnetic field
m: magnetic quantum number
s 0
continuous particle
-1 0 1
p 1
mass charge
d 2 (Thomson, 1897; mass-to-charge ratio) (Millikan, 1910)
me = 9.1*10-31 kg e = -1.6*10-19 C
f 3
shells
s: sharp;
discrete subshells
p: principal;
(quanted) d: diffuse;
f: fundamental. see light emission
measurement wave
n: principal quantum number
• Principle of minimum energy Davisson and Germer, 1927 diffraction of fast electrons electron
an electron’s possible energy
• Pauli exclusion principle through a gold foil microscope
levels in the hydrogen atom 7 8

The electron as a wave The propagation law of free electrons

v1
λ
lk k k  1,2,...
v2
2
only discrete values
are allowed! wave package

state of motion in classical mechanics slower and faster propagation of an electron

λ: wavelength of the
matter wave the state function is
not a periodic function
h h
λ 
l p me   v
analogy: Stationary waves of a stretched string De Broglie, 1923

position of a classical object can be determined exactly the state function of the electron
The state function of the electron:

ψ(x,t) ψ(x,t) will disperse

while propagating
(Schrödinger)
• location (x): where ψ(x,t)=1

• momentum (p): ”shape” of ψ(x,t) 9 10

Textbook page 44-51

The electron bound in an atom Atomic interactions
Δx
in the electric field of the outer shell
nucleus
atomic nucleus (or proton)
short range long range
interaction: interaction:
repulsion between coulombic attraction
nuclei
deformed state function (electron cloud overlap) inner shell

Δp~Δ(1/λ)
Δ(1/λ) ≥ 1/Δx
The Heisenberg uncertainty relation repulsion equilibrium attraction
the uncertainty of the momentum (Δp) in the (inner shells and nuclei) attraction = repulsion (outer shells)
case of a free electron:
”one-dimensional H-atom”
Δx  Δp  h
Δt: uncertain, so E can be certain:
ΔE  Δt  h discrete energy levels
11 12

2
 Atomic interactions Primary bonds
intramolecular intermolecular
E pot  Eattraction  Erepulsion strong weak
primary secondary
A B
E pot    • covalent: common electron state around the
rn rm participating nuclei, strong: Eb>1eV type depends from
repulsive electronegativity
• metallic bond: multi-atomic system, Eb>1eV (EN)
A, B: interaction-specific constants
• ionic bond: Coulomb-forces between ions, Eb>1eV EN = │Ei │+ │ Eea │
(atom-dependent)
ionization electron-
Eb
n (attraction) < m (repulsion) energy affinity

attractive
r0: binding distance

Eb: binding energy

EN values according to
Pauling
13 14

Secondary bonds 1 Secondary bonds 2

• Van der Waals: between two apolar atoms (without permanent dipole moment)
• Dipole-dipole interaction:
where a temporarily created dipole interacts with an apolar molecule or atom thus
converting it into a dipole (induced dipole) • Constant charge distribution

• Van der Waals radius: r0=rA+rB is present in a (given part of

• Intermolecular or intramolecular a) molecule

• Important biological role: formation of organic structures • Partially (+) and (-) segments
• Weak: (Eb ~ 0,02 eV) are held together by
electrostatic interactions
fluctuation ion-dipole induced dipole (Coulombic forces)
Eattraction = p * E
• Intra/intermolecular

• Weak interaction (Eb = 0.003- p: dipole momentum (p=Q*d)

E: electric field strength generated by the

0.02 eV)
surrounding partners

15 16

Textbook page 573

Secondary bonds 3 Atomic force microscope (AFM)

2. bending of a tiny
1. Van der Waals
• H-bond: the H-atom interbridges two other cantilever is
between the
measured with a
atoms (F, O, N) of high electronegativity atoms of a
laser projected
sample and a
• r ~ 0.23-0.35 nm onto it
sharp tip
• E ~ 0.2 eV
DNA water

• Hydrophobic interaction: weak Van der Waals

interaction (Eb = 0.003-0.02 eV), thermal
motion (kT~0.025 eV) could disrupt the
system atomically
smooth surface 3. scanning in X-Y-Z
• ordered water molecules exclude the (mica)
lipids in water directions by precisely
apolar structures (minimized contact moving either the
sample or the tip
surface) 17 18

3
 AFM operating modes
Contact mode AFM
• Contact: the tip touches the surface, the
deflection of the cantilever (i.e. the force
cantilever exerted on the sample by the tip) is held
constant.
tip • Z-feedback system: deflection is
maintained at a constant value
sample (setpoint) by lifting or lowering the
cantilever.
• topography data (i.e.: height) in each
x;y point is calculated from these Z
sample surface movements
• Non-contact: the cantilever is oscillated
without contact with the surface: resonant contact
contact frequency (f0) and the amplitude of the
oscillation changes with surface
topography.
• Z-feedback: maintains the amplitude
non-contact by lifting or lowering the oscillating
cantilever.
19 20

Practice: Resonance

Contact mode AFM Non-contact/oscillating mode AFM

suitable for soft Resonance: a driven oscillation occurring when the oscillatory system is exposed
biological samples to a driving force with a frequency close to its eigenfrequency (f0). Amplitudes may
(e.g. cells) quadrant
become extremely large.
laser photodiode

U0
U1

d ~ force

F = force = D d
force / elasticity
d: deflection measurement on
D: spring constant biological samples

21 22

Non-contact/oscillating mode AFM Cantilevers

• Material: mainly silicon nitride

• Tip radius: 0.1 nm- 100 µm

• Spring constant ~ 0.1-10 N/m

• fo ~ 50-500 kHz

Position (mm)
0 20 40 60 80
Amplitude (mm)

0
-10
-20
-30 1 D
-40 f0 
-50
-60
2 m
23 24

4
 Principle of scanning: piezoelectricity AFM - properties
• Main advantages:
• 3D surface profile.
• Images are collected with ~10 pm vertical and somewhat worse horizontal
resolution.
• Any surfaces (conductors, insulators and semiconductors) can be imaged.
• Works in ambient air, special gas or in fluid environment as well.
• Usually does not require fixation or staining of the sample.
• Biological samples can be examined in their native state and physiological
• direct piezoelectric effect: deforma on → voltage environment.
• inverse piezoelectric effect: voltage → deforma on • Main disadvantages:
• Samples must adhere to a substrate. Surface adhesion may lead to distortion.
• X, Y, Z axis piezo: e.g. 150 V → 40 µm 0.1-nm-accuracy
possible
• Slow scan speed.
• Scan height limited to few microns („the flatter the better”).
• Scan size limited to few tens of microns.
• High cost.
25 26

Images recorded in our lab at the Department Pentacene molecule

electron current through the tip (STM)

500 nm

AFM images (tip covered with CO)

200 nm

AFM cantilever

AFM tip

Nature Chemistry 1, 597 - 598 (2009)

27 28

Visualizing chemical reactions

Thank
you
for your attention!

???!!?!

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