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Lecture 11
Lecture 11
Daniele Passerone
Empa, Swiss Federal Laboratories for Materials Science and Technology
Ueberlandstrasse 129, 8600 Dübendorf
daniele.passerone@empa.ch
Scanning
tunnelling
microscope
(STM)
•An
instrument
for
imaging
surfaces
invented
in
1981
by
Gerd
Binnig
and
Heinrich
Rohrer
(at
IBM
Zürich):
Nobel
prize
in
physics
1986
•more
than
30
years
later,
the
most
advanced
nanotechnology
center
@
IBM
Rüschlikon
was
dedicated
to
their
name
Tunnelling
effect
and
STM
2.
• Stable and sharp metal tip (single atom) 3.
4.
5.
Metal
electrons
Sill
levels
Specimen
and
tip
are
A
voltage
is
applied
and
until
Fermi
energy,
and
brought
close
separated
electrons
can
tunnel
from
the
minimum
energy
to
by
vacuum the
specimen
to
the
tip
or
extract
an
electron
is
viceversa
called
work
function
Tunnelling
and
available
states
•The
tunnelling
current
decays
exponentially
with
the
distance
from
the
sample
(note:
𝚽
is
the
work
function
of
the
sample)
•Since
the
current
decays
typically
by
one
order
of
magnitude
every
angstrom,
this
makes
STM
very
sensitive
to
surface
corrugation
at
the
atomic
level
Maintaining
a
constant
tunneling
current
by
adjusting
the
height
with
a
piezo-‐
electric
crystal,
and
monitoring
the
piezo
voltage
while
scanning,
allows
one
to
image
a
surface,
under
ideal
conditions,
to
atomic
resolution.
How
to
compute
the
tunnelling
current
First-‐order
perturbation
theory
for
the
transition
rate,
counting
all
possible
initial
and
Sinal
states
Corrugation
and
electron
density
One
of
the
factors
affecting
resolution
is
corrugation,
i.e.
how
much
the
electron
density
of
surface
atoms
varies
in
height
above
the
surface.
Graphite
has
a
large
corrugation,
and
is
very
planar,
and
thus
is
one
of
the
easiest
materials
to
image
with
atomic
resolution.
(see
next
slide
for
example)
STM
does
NOT
probe
the
nuclear
position
directly,
but
rather
it
is
a
probe
of
the
electron
density,
so
STM
images
do
not
always
show
the
position
of
the
atoms.
STM
imaging
depends
on
the
nature
of
the
surface
and
the
magnitude
and
sign
of
the
tunneling
current.
For
example,
if
you
have
Cu
and
Si
on
the
same
surface,
under
the
same
condition,
the
current
with
Cu
is
much
higher
.
Since
STM
images
the
outermost
atom
on
sample
surface,
ultra
high
vacuum
(UHV)
is
normally
required
to
assure
no
surface
contamination
(e.g.,
coverage
of
air
molecules
or
water)
so
as
to
image
single
atoms
or
at
atomic
resolution)
Examples of STM images
•Allows to obtain images of surfaces up to atomistic resolution.
•Huge importance in the development of nanoscience over the past 30 years
(Nobel prize award 1986).
Ruffieux et al., Empa laboratories (2010)
A layer of h-BN is deposited on Rh(111), forming a periodic nano mesh with wires and pores.
Molecules show preferential adsorption and orientation.
Tersoff-‐Hamann
and
density
of
states
Limitations
of
simple
theory
Corrugated
Flat surface: sample:
Single s-orbital Single s-orbital
is ok description might
be not sufficient
The actual geometry of the tip used for scanning is usually not known.
Models explicitly including tip geometries should not be too computationally
demanding for applications to large systems.
Modeling finite size tips
•Using a two atoms tip the tunneling current is proportional to the sum of the sample LDOS
at the position of the two atoms R1,R2 *:
*R.Gaspari, C.A. Pignedoli, R. Fasel, M. Treier, D.Passerone, Phys. Rev. B 82, 041408(R) (2010)
Application to HBC on Cu(111)
•Large scale DFT calculations on stepped HBC/Cu(111)
surfaces
21
22
23
24
25
26
27
28
29
30
31
Infrared
spectroscopy
Spectroscopies
•Methods
to
study
the
properties
of
matter
(atoms,
molecules
and
solids)
by
investigating
its
interactions
with
particles
(photos,
electrons,
neutrons,
ions).
•We
consider
here
today
and
next
time
in
particular
infrared
and
ultraviolet
(UV)
spectroscopy:
interaction
of
photons
with
matter.
Infrared
spectrum
Examples:
IR
(diatomic molecule)
Atomic
structure
vs.
molecular
vibrations
•The
presence
of
certain
functional
groups
can
easily
be
tested
through
vibrational
spectroscopy
•Intensities
for
IR
(and
Raman)
are
obtained
from
the
derivatives
of
the
dipole
moment
and
polarizability,
along
the
normal
mode
vectors
in
such
static
calculation
•Problem
in
condensed
phase:
Static
calculations
need
to
be
started
from
an
optimized
minimum
of
the
PES:
molecules
in
the
gas
phase
•In
general
linear
molecules
have
3N-‐5
normal
modes
(three
for
the
center
of
mass
translation,
two
rotational
angles);
non-‐linear
molecules:
3N-‐6
normal
modes
•Harmonic
oscillator:
we
need
to
obtain
the
unknown
force
constant
from
the
potential.
Hooke’s
law:
dV 1 2
F = = kx ! V = kx
dx 2
•Newton’s
law:
d2 x
m 2 = kx ! x(t) = A sin(2⇡⌫t)
dt
•Specify coordinates of each atom and the differences to the equilibrium positions:
•Use
classical
or
ab
initio
is
used
to
compute
V
as
a
function
of
the
coordinates…
and
thus
second
derivatives
as
a
function
of
the
displacement
V (x1 , y1 , z1 , x2 , y2 , z2 , . . . , xN , yN , zN )
•We
sample
the
change
in
the
forces
as
we
move
the
different
atoms
in
different
directions:
Hessian
diagonalization
•The complete list of the force constants is called the Hessian:
•Let
us
consider
a
linear
molecule
and
only
vibrations
along
the
axis
(symmetric
and
antisymmetric
stretching
modes):
Hessian
diagonalization
•The
eigenvalues
are
the
negative
of
the
squared
normal
mode
frequencies
•The
eigenvectors
are
the
mass-‐weighted
coordinated
displacements
In
quantum
mechanics…
•Vibrations
are
quantised
along
each
mode.
The
fundamental
frequency
is
the
one
obtained
by
the
classical
analysis…
but
the
energy
levels
and
eigenvectors
for
each
mode
are
given
by
the
Schrödinger
equation
(Hn
are
Hermite
polynomials)
Note
on
energy
•If
a
certain
normal
mode
has
a
certain
energy,
then
E~k
A^2
with
A
maximum
amplitude
of
an
oscillation.
•If
all
modes
have
the
same
energy
(energy
equipartition)
it
follows
that
the
amplitude
is
inversely
proportional
to
the
eigenfrequency
and
inversely
proportional
to
the
square
root
of
the
reduced
mass
m.
•So
in
order
to
obtain
a
spectrum
with
the
same
intensity
in
the
each
mode,
we
need
to
rescale
the
spectrum
accordingly.
IR
spectroscopy
•In
an
IR
spectroscopy
experiment
we
introduce
light,
an
electromagnetic
wave,
which
interacts
with
a
molecule
by
disturbing
the
local
electric
Sield
EF.
The
energy
of
the
photon
must
match
the
difference
in
energy
between
two
vibrational
states.
•The
strength
of
the
absorption
depends
on
the
initial
and
Sinal
state,
and
on
the
dipole
moment
of
the
molecule
•The
dipole
moment
is
modiSied
during
the
vibration:
Taylor
expanding
around
equilibrium…
•For
small
vibrations,
we
keep
the
Sirst
order
and
we
note
that
the
transition
between
states
will
depend
on
the
derivative
of
the
dipole
moment
(the
Sirst
term
is
zero
for
state
orthonormality)
Autocorrelation
functions
•All
vibrational
spectra
calculated
from
molecular
dynamics
simulation
are
based
on
the
Fourier
transform
of
certain
autocorrelation
functions:
connecting
the
autocorrelation
in
time
domain
with
the
Fourier
transform.
Intensity
of
the
peaks
of
the
infrared
spectrum
•In
static
calculations,
the
intensities
of
a
mode
are
given
by
the
square
of
the
derivative
of
the
dipole
moment
along
the
normal
coordinate
of
that
mode
•In
molecular
dynamics,
we
should
keep
in
mind
that
in
harmonic
approximation
if
the
run
is
well
equilibrated,
each
oscillator
contains
the
same
amount
of
energy
(equipartition)
•The
amplitude
of
a
mode
is
inversely
proportional
to
the
eigenvalue
frequency
ω
and
to
the
square
root
of
the
mass,
so
to
obtain
the
same
intensity
for
each
mode
one
should
rescale
the
spectrum
by
ω2,
which
is
formally
equivalent
(and
numerically
more
convenient)
to
correlating
time
derivatives
(Fourier
transform
properties).
•In
the
particular
case
of
the
infrared,
we
autocorrelate
the
derivative
of
the
dipole
moment
Examples:
methanol
and
acetone
For
faster
MD
(less
accurate):
Density
functional
tight
binding:
DFTB
•DFTB is based on Density Functional Theory (DFT) but uses empirical approximations to improve the performance
whilst maintaining accuracy.
•The main approximation in the tight- binding approach is the replacement of the exact many-body Hamiltonian in DFT
with a parameterized Hamiltonian matrix. In the DFTB description pseudo atomic wave functions, written in terms of
Slater-type orbitals and spherical harmonics, are used to model the electron density.
•The orbital basis is fitted against DFT theory and then used to calculate the Hamiltonian and overlap matrix elements. The
DFTB approach uses approximations to expand the total energy of the DFT representation to the second order in charge
density and spin density fluctuations.
•The
matrix
elements
do
not
fully
describe
the
total
energy
of
the
system,
the
remaining
part
of
the
total
energy
is
included
as
a
short-‐range
repulsive
term
which
can
be
described
in
terms
of
pair
wise
potentials
between
atoms.
The
pair
wise
potentials
are
acquired
through
a
Sitting
process.
•For
systems
where
the
balance
of
charges
between
pairs
of
atoms
is
very
small,
DFTB+
also
uses
self
consistent
charge
(SCC-‐DFTB)
to
improve
the
description
of
the
bond.
In
order
to
simplify
the
calculations,
the
SCC
calculation
is
performed
on
Mulliken
charges
rather
than
the
potential
and
charge
density