Politecnico di Torino

Nanoscale sensing elements and device production

Molecular Electronics
A guide to the labs

Azzurra Pulimeno, Ali Zahir

September 2, 2013

CHAPTER 1

Lab 1 - Introduction to ab-initio simulations

and electron transport in molecular transistor
1.1

Login

HOW TO LOGIN

1.1.1

Suggestions

During this lab you will perform a lot of simulations with different tool for molecular
electronics and some simulations will take long time. In order to optimize your time
and complete all the exercises, here you have a suggested scheduling:
Perform the excercise from step 1.2 to step 1.6, as they follow.
While the simulation of exercise 1.6 is running, perform the exercises linsted in
Section 1.7 from step to 1.5.
When the simulation of exercise 1.6 is finished, complete the step 1.6.
Complete the step 1.6 for all the exercises of Section 1.7.

1.2

Avogadro: a brief introduction

Avogadro is a free software for molecule editing and visualizing. The tool is installed
in the following path: /tools/Avogadro. In order to run the software type in the shell
the command ./avogadro and wait untill the graphical interface is open (see Fig.1.1).
If the setting area is hided, press the button Display settings shown in Fig.1.2
(enlarge the main window if you cant find the button). In the same figure you can see
the main tool bar for selecting among different modes: for example, the first on the
left allows you to draw a molecule, selecting the atom and bond type; clicking on the
second button on the left you have the possibility to change the viewpoint in the work
space, zoom in or zoom out and so on. For each button, while moving the mouse on it
an help window appears.
1

Molecular Electronics

Figure 1.1: Avogadro GUI

Figure 1.2:

1.3

Thiophene molecule

The first exercise focuses on the thiophene molecule, a simple system you will reuse
in the following lab sessions. Thiophene is the starting block for a set of conductive
molecule called oligothiophene. Since this molecule is a basic block for many applications and molecular systems, usually you can find its structure ready to use in a
data base. This is our case, in fact Avogadro provides a library of basic molecules
and you can find it in this directory: /tools/Avogadro/share/avogadro/fragments. Here
you can find a set of so called fragments, divided according to the organic chemistry
classification. In particular the thiophene molecule belongs to the heteroaromatics.
Importing a fragment from the database requires a simple procedure, for the thiophene click on File and select Import Molecule File: a small window opens
and here you can type the path of the molecule (/tools/Avogadro/share/avogadro/fragments/heteroaromatics/thiophene.cml ) or select it browsing the filesystem and then
click on Open and the thiophene ring will appear on the workspace (see Fig. 1.3).

Figure 1.3:
The formulation is C4 H4 S and its structure and symbol are in Figure 1.4. Lets

Molecular Electronics

analyze the structure. From the mail Avogadro manu select: View Properties
Molecule The total molecular weight and the dipole moment: write them down, so
that later you can compare them to other data.
Now analyze the properties of the atoms:View Properties Atom Analyze
each atom name and reconize it in the displayed molecule and the type of ligand. It is
interesting to note the bond properties, where you have the number of the interested
atoms and the bond length.
You can display the dipole vector by clicking the Dipole box in the left menu.

Figure 1.4:
This molecule will be used as conductive molecule, so you need to add two thiols for
further bonding to the gold electrodes. Firstly, in the browsing mode reorientate the
molecule so that the sulfur atom (the yellow ball) is at the top; then, switch to drawing
mode (click the pencil in the toolbar) and in the setting list (press tool settings) select
the sulfur (16) as element, single for bond order and select Adjust Hydrogens tick.
Now, add the thiol group clicking on both the top hydrogens; after clicking on it they
will be changed in thiol as shown in Fig. 1.3.
Did the dipole vector change? In which direction? Did it change in terms of value
as well?

Figure 1.5:
Again analyze the molecule properties View Properties Molecule and
notice the change; analyze the atom and bond properties. In particular annotate the
distances of the added bonds and the charge of the interested atoms.
Now an optimization is needed: press from the main menu Extensions Optimize geometry The new bonds with thiol are now optimized: using angain the view-

Molecular Electronics

properties menu, analyze what changed for the whole molecule (energy and dipole),
for the added ligand (distance and charge).
Note the dipole vector variation.
The following step is optimizing the molecule so that the final structure corresponds
to the lowest energy (for simple structures this should be similar to the previously
executed optimization). Performing an optimizion requires more sofisticated tools for
computational chemistry; the most common is an ab-initio simulator and Avogadro
allows to interface with it, genereting an input file with the main settings.
In order to do it, from the main menus select Extensions Gaussian. A new
window appears, fill the form as shown in Fig.1.6: Geometry Optimization as calculation, B3LYP as theory, 3-21G as basis and Z-matrix as format. Specify the title you
prefer and click on Generate. Browse the filesystem in order to choose a directory in
your home, insert the file name you prefer and click on Save. The file is now ready
to use in the ab-initio simulator, the meaning of its content will be discussed in the
following section.

Figure 1.6:

Summary of what is requested at the end of this exercise

Molecules properties, nod characteristica, noticeable differences of molecule before and
afte the thiol and the optimization. File with the final Z matrix for the thiolated
thiophene.

1.4

The Z matrix

Several format are used to describe molecules and compounds. As the Z matrix is
among the most diffused and is the input for the ab-initio simulator, a good analysis
of the Z matrix is mandatory.
Using your preferred text editor (for example gedit), open in read mode the input
file genereted by Avogadro for the thiophene molecule (for example thiophene.com).

Molecular Electronics

The first three rows looks like the followings:

#n B3LYP/321G Opt
thiophene molecule optimization
0 1

The first row specifies the procedure and basis set we want to use for this calculation
(BLYP3) and an optimization step. This is called route section. Lines in the route
section begin with a # sign. Sometimes a letter follows. For example the T requests
terse output from the program (only the essential results), # alone or # n requests
normal (traditional) Gaussian output, and #P requests the maximum amount of detail
in the output file. All route sections must include a procedure keyword and a basis
set keyword. Additional keywords further specify the type of calculation desired and
additional options.
The second line is the tile section and it contains a brief (usually one-line) description of the job. The title section appears in the output and is stored in the ab-initio
simulator archive entry but it is not otherwise used by the program.
The third section (third row) specifies the structure of the molecule system to be
investigated. This section holds the charge on the molecule and its spin multiplicity.
Each of them is entered as an integer on this line, with one or more spaces separating
them. Since our one is a neutral molecule, its charge is 0. Spin multiplicity refers
to the arrangement of the electrons within the molecule. Thiophene has no unpaired
electrons, so it is a single and its spin multiplicity is 1
One of the following parts is the molecule specification. The Molecule Specification
section holds the type and positions of each of the atoms in the molecule.
C
C
C
C
S
S
H
H
S
H
H

1
2
3
1
1
2
3
4
9
6

B1
B2 1 A2
B3 2 A3 1
B4 2 A4 3
B5 2 A5 3
B6 1 A6 3
B7 2 A7 1
B8 3 A8 2
B9 4 A9 3
B10 1 A10

D3
D4
D5
D6
D7
D8
D9
2 D10

The values are referred to with letters in the matrix; the values associated to the
letters are speicfied in the last section:
Variables :
B1
1.36576
B2
1.43629
A2
112.20614
B3
1.36576
A3
112.21506
D3
0.02562

Molecular Electronics
B4
A4
D4
B5
A5
D5
B6
A6
D6
B7
.
.
.

1.72483
112.09401
0.02562
1.08848
125.67869
179.97438
1.09002
125.03930
179.97438
1.09001

Considering for example the third carbon atom (C), it is connected to the second
carbon atom and the length of the bond is defined by the variable B2 specified later
and expressed in
A; moreover, this atom forms an angle of A2 degrees with the first
carbon atom (and obviously with the second already mentioned).

1.5

Ab-initio simulations: a brief introduction

Computational chemistry is a branch of chemistry itself that allows chemists to study

chemical phenomena by means of computer simulations rather than experimental processes. So, starting from the fundamental laws of quantum mechanics, an ab-initio simulation predicts the energies, molecular structures, vibrational frequencies and molecular properties of molecules and reactions in a wide variety of chemical environments.
In particular, given a molecular system, its energy and other molecular properties
could be obtained by solving the Schrodinger equation:
H = E

(1.1)

Since this equation has an exact solution only for the hydrogen atom, some mathematical approximations are needed for any other molecules or systems. Computational
chemistry provides three classes of approximation methods for solving the Schrodinger
equation:
Semi-empirical methods: they use sets of parameters derived by experimental
data to compute a solution.
Ab-initio methods: their computations base mainly on the laws of quantum mechanics and a set of physical constants (the speed of light, masses and charges of
electrons and nuclei, Planks constant).
Density Functional Theory (DFT) methods: they are similar to ab-initio methods,
but they include the effects of electron correlation (the fact that electrons in a
molecular system react to one anothers motion and attempt to keep out of one
anothers way). Ab-initio calculations consider this effect only in an average

Molecular Electronics

sense (each electron sees and reacts to an averaged electron density), while DFT
methods account for the instantaneous interactions of pairs of electrons with
opposite spin.
Each method is characterized by the combination of theoretical procedure (hereinafter called method ) and a basis set. An example of method is Hartree-Fock (HF)
for ad-initio methods and B3LYP for DFT. A basis set is a mathematical representation of the molecular orbitals within a molecule. The basis set can be interpreted
as restricting each electron to a particular region of space. Larger basis sets impose
more accurately approximate molecular orbitals. They require correspondingly more
computational resources, as weel as more accurate methods become correspondingly
more expensive computationally.
In the previous section, you analysed the structure of an input file for ab-initio
simulation. Now lets run it! In order to set the enviroment type in the shell the
command ./ab-initio; now you are ready to run a computation using the following
command: /usr/local/g09/g09 your file.
Pay attention that all the output files will be saved in the directory where you run
the command.

1.5.1

Thiophene molecule

In the previous exercise, you generated the input file for the ab-initio simulation of a
thiophene molecule. Now use it to run the computation, using the command:
/usr/local/g09/g09 thiophene.com
The computation will last few minutes, in the meanwhile start Avogadro and, once
the simulation is completed, open the ab-initio simulation output file (for example,
thiophene.log). Following the instruction of the previous, analyze the thiophene properties (molecule proprerties, bond lenght and angle), comparing these new data with
the results obtained with Avogadro in the previous session.
Without closing Avogadro (open a new terminal!), type the following command:
/usr/local/g09/formchk thiophene.chk thiophene.fchk
where instead of thiophene.chk you have to insert the name of your checkpoint file and
instead of thiophene.fchk you can choose the file name you prefer, keeping the .fchk
extension.

1.5.2

HOMO - LUMO analysis

On Avogadro, open the .fchk file and have a look at the molecule. The checkpoint
file contains all the information of energy and molecular orbitals, so it is possible to
create some surfaces associated for example to the HOMO (Highest Occupied Molecular
Orbital) and LUMO (Lowest Unoccupied Molecular Orbital). From the main menu
select Extensions Create surfaces.. and in the small window that opens select
Molecular Orbital and HOMO both for Surface Type and Color by (see Fig.1.7) and
click on Calculate; repeat this step selecting LUMO.

Molecular Electronics

Figure 1.7:
You can calculate and visualize the surfaces for all the other molecular orbitals
(MO).
In order to compute the energy level related to one molecular orbital (it is required
in the following exercises), open the output file (for example thiophene.log) with a text
editor: starting from the end of the file scroll up till reaching the Population analysis
using the SCF density section, as in the following example:

P o p u l a t i o n a n a l y s i s u s i n g t h e SCF d e n s i t y .

O r b i t a l symmetries :
Occupied (A) (A)
(A) (A)
(A) (A)
(A) (A)
Virtual
(A) (A)
(A) (A)
(A) (A)
(A) (A)
The e l e c t r o n i c s t a t e i s
Alpha o c c . e i g e n v a l u e s
Alpha o c c . e i g e n v a l u e s
Alpha o c c . e i g e n v a l u e s
Alpha o c c . e i g e n v a l u e s
Alpha o c c . e i g e n v a l u e s
Alpha o c c . e i g e n v a l u e s
Alpha o c c . e i g e n v a l u e s
Alpha o c c . e i g e n v a l u e s
Alpha v i r t . e i g e n v a l u e s
Alpha v i r t . e i g e n v a l u e s
Alpha v i r t . e i g e n v a l u e s

(A) (A) (A) (A) (A) (A) (A) (A) (A) (A)
(A) (A) (A) (A) (A) (A) (A) (A) (A) (A)
(A) (A) (A) (A) (A) (A) (A) (A) (A) (A)
(A) (A) (A) (A) (A) (A)
(A) (A) (A) (A) (A) (A)
(A) (A) (A) (A) (A) (A)
(A) (A) (A) (A) (A) (A)
1A.
88.28441 88.26912
10.15085 10.14966

5.89513 5.89071

5.87799 5.87792

0.81440 0.77290

0.56333 0.51022

0.39283 0.37052

0.27275 0.26507

0.02126 0.00235

0.06049
0.06632

0.28856
0.32847

(A) (A) (A) (A)

(A) (A) (A) (A)
(A) (A) (A) (A)
(A)
88.26904 10.20794 10.20785
7.92485 7.91198 7.91173
5.88361 5.88291 5.88264
5.86898 5.86898 0.90165
0.74914 0.69470 0.56489
0.45216 0.44494 0.40260
0.36072 0.35459 0.32619
0.21145
0.00511
0.01576
0.02837
0.10236
0.17591
0.18349
0.38791
0.40644
0.47321

This part of the files shows the occupancy of the molecular orbitals and their eigenvalues, for both the occupied (occ. in the file) and the unoccupied (virt.) orbitals. The
values provided here are in atomic unit, so you need to convert the eigenvalue in eV,
multiplying it by 27.211. In the example reported above, the HOMO (the last occupied
orbital) has an eigenvalue equal to -0.21145, multiplying it times 27.211, the energy
level of the HOMO will be -5.753 eV.

Molecular Electronics

Compute the energy levels for both HOMO and LUMO of your molecule and write
them down.

1.6

Atomistix Tool Kit (ATK) - Virtual NanoLaB

(VNL)

Atomistix ToolKit can model the electronic properties of closed and open quantum
systems based on density-functional theory (DFT) using numerical basis sets. In our
simulation, Au-molecule-Au molecular system is considered as an open system. For
such systems, Non Equilibrium Greens Function (NEGF) is used to calculate the
density matrix and other transport properties. The goal of this exercise is to calculate
the transmission spectrum of conductive molecules, starting from the thiophene bonded
to a gold nanogap and without bias voltage between the gap extremities.

1.6.1

Database and Molecule Builder

In order to run the software type in the shell the command ./vnl
In main VNL window click on Builder. Now in the Builder window click Add
/ From Database / Databases / Molecules / Polythiophene. And double click
on the molecule. The molecule should ready be to be prepared as shown in the
figure 1.8

Figure 1.8: The Builder window with the molecule of thiophene imported from the
Database

1.6.2

Molecule Preparation for the Optimization

CTRL + A to select all the molecule atoms. Click on Coordinate Tools / rotate
/ perform the necessary rotations up to the molecular plane is parallel to the z-y
plane and the molecular base, opposite to the sulfur atom, is parallel to the z
axis.
Changing Hydrogen atoms to Sulfur: in the Coordinate Tools left click on cordinate list. Click on the hydrogen to change: the correspondent row of the table on
the left is now highlighted. Double click on the hydrogen atom and select Sulfur

Molecular Electronics

10

from drop down menu. You can see the result of the last two points in the figure
1.9.

Figure 1.9: The Builder window with the molecule of thiophene well rotated and
missing two atoms of hydrogen

Adding Hydrogen to newly added sulfur atom: right click on the atom table
on the left / Insert Element. Double click on the name of the new elements
(Hydrogens) / change the type with Sulfur / set the coordinates of the sulfur
to be close to the correspondent hydrogen, a bond should appear between the
hydrogen and the sulfur if they are close enough. Add one more Hydrogen and
set its cordinates to bond the Sulfur. The final result is showed in the figure 1.10

Figure 1.10: The Builder window with the molecule of thiophene and the thiol groups

1.6.3

Molecule Optimization-Script Generator

In the Builder window compose: click on the arrow located in the lower right hand
corner of the window / Script Generator / double click on New Calculator. Also
in the same Script Generator window double click on Optimization / Optimize
Geometry. Type the name of the output file in the Default output file box (for
example opt-lab1 ) and select the path in your home (the destination folder). At
this point the window should appear as in the Figure 1.11. Double click on the
script New Calculator. The list of calculator settings is to define the parameters
and the methods (type of solver) of the calculation. In this tutorial you will

Molecular Electronics

11

modify: Calculators / Basis set/ exchange correlation / Single zeta all over as
shown in Figure 1.12.

Figure 1.11: The Script Generator window in the optimization process

Figure 1.12: Setting the parameters of the optimization process

1.6.4

Molecule Optimization-result using VNL

In the Script Generator window compose: click on the arrow located in the lower
right hand corner of the window / Job Manager/ Run Queue.

Figure 1.13: Job Manager window

After the optimization the output file with .nc extension (for example opt-lab1.nc)
is saved in the destination folder. In VNL Menu bar / double click on the Viewer
/ Drag and drop the file (for example opt-lab1.nc) to the Viewer window. Now
you should be able to see the optimized molecule as showed in the Figure 1.14.
Once simulation is completed you will get the optimized molecule. You can check
the Z-matrix of optimized molecule. To do it, in Builder window click Coordinate tools
/ Z-matrix. In the Z-matrix table of optimized molecule (Figure.1.15) d is the distance

Molecular Electronics

12

Figure 1.14: VNL optimization of the molecule

Figure 1.15: Z-matrix of optimized molecule using VNL optimization

(A0 ) between two atoms, is the bond angle and is dihedral angle. Compare this
table with the Z-matrix obtained using gaussian optimization.
As the VNL optimization will take some time, so while this simulation is in execution you can proceed to the next step with optimized file (1TT-S.py) of the same
molecule in your home directory.

1.6.5

Molecular Junction Building

So far you have learnt how to optimize molecule using VNL optimizer. Now you will
learn how to use the Molecule Device Builder in VNL to construct molecular junctions
i.e. a molecule embedded between two gold (111) surfaces.
Open Builder, click Add / From File / the optimized molecule (1TT-S.py). In
next step the molecule will be bound to electrodes through left and right sulfur.
This needs respective Hydrogen (near to sulfur atoms) atoms to be deleted.
Open a Virtual NanoLab main window / tools / custom Builder / Builders /
Molecular Junction. Drag and drop of the contents of the Builder window, from

Molecular Electronics

13

the builder drag and drop icon to the drop configuration here subwindow in the
Molecule Device Builder window, as shown in the Figure 1.16 by the arrow.

Figure 1.16: Drag and drop of the molecule from the Builder to the Molecular Device
Builder
We want to connect the molecule to the electrode through the sulfur atoms. In the
Molecule Device Builder, the two left and right adsorption boxes allow to insert
the number of the atom in the molecule that we want to use for this purpose.
Using the Coordinate list of the Builder you can identify the atom number of
the sulfur to be connected in the left and in the right position. Set the left and
the right adsorption atoms accordingly and the result should be the same of the
Figure 1.17.

Figure 1.17: The molecular junction

1.6.6

Script Generator of the Molecular Junction Transport

problem

In the Molecular Device Builder window compose: click on the arrow located in
the lower right hand corner of the window / Script Generator. In the Default
output file box type the name for the output file (for example 0bias-lab1.nc) and
select the destination folder. Double click on New Calculator / New Calculator.
The list of calculator settings is to define the parameters and the methods (type

Molecular Electronics

14

of solver) of the calculation. In this tutorial you will modify: Calculators / ATKDFT, Basic Device / Left Electrode Voltage = 0V / Right Electrode Voltage =
0V as shown in the Figure 1.18. Calculators / Basis set/exchange correlation /
Single zeta all over as shown in the Figure 1.19. Click on OK. In this way you
will find the transmission spectrum of the the molecular system in equilibrium,
which will be then used to find I-V characteristics of molecular FET.

Figure 1.18: Basic Device parameters of the molecular junction

Figure 1.19: LCAO basis set parameters of the molecular junction

In the Script Generator window, double click on Analysis / Transmission Spectrum. Double click on transmission spectrum , set the Energy Range, for instance
between -3 eV and +3 eV, as shown in Figure.1.20.

1.6.7

Job Manager of the Transport problem

In the Script Generator window compose: click on the arrow located in the
lower right hand corner of the window / Job Manager/ Run Queue,, as shown in
Figure.1.21.

Molecular Electronics

15

Figure 1.20: Setting the Transmission Spectrum parameters

Figure 1.21: Job Manager window of the Transport Problem

1.6.8

Analyzer of the I-V characteristic

When the Job Manager computation is finished, you can find the result file (for
example 0bias-lab1.nc) in the destination folder. Open Virtual nanolab window
and click on the file (0bias-lab1.nc) / in result browser click on Transmission
spectrum / in result viewer click on plot show. You can also save the result by
clicking on Export save.
The nearest peaks above and below the fermi energy level f in the transmission
spectrum corresponds to LUMO and HOMO of the molecular system, respectively. Write them down as this information will be needed later in the I-V
analysis of the system.

Figure 1.22: Result of the analysis

Molecular Electronics

1.7

16

Other molecules

Transmission function has an important role in determining I-V characteristic of molecular FET. Different molecules have different transmission spectrum. It is also dependent on the type bonding atom between molecule and electrode. In this exercise you
will calculate transmission spectrum of different conductive molecules.
Repeat the previous exercises considering the following conductive molecules:
Thiophene with Oxygen (O) atoms as binding elements instead of Sulfur (S);
Benzene molecule (you can find it in the database, it belongs to the aromatics
family) with Sulfur atoms as binding elements;
For sake of brevity, in your home folder you can find the optimized structures of
these molecules ready to be used.

1.7.1

Importing Optimized Molecular Structure to VNL

In the Builder window click Add / From File / Browse to the file (for example
1T T O.py) and click open it.

1.7.2

Molecular Junction Building

As this is the optimized structure of the molecule, so you can skip the steps of
building and optimization of the molecule . You can continue directly from step
1.6.5 and find transmission spectrum for each molecule.
NOTE: In case of Oxygen atom as binding element, initially, there will be no
direct binding between gold electrode and the molecule. In order to bind molecule
to electrode, change the value of the Adsorption height of left surface and
right suface in the molecular device window from 1.9 to 1.54.

1.7.3

Script Generator

This point is equivalent to the Script Generator point of the previous exercise.
Repeat the steps for all molecules and save the transmission spectrum file in .txt
formate. Also write down the HOMO and LUMO information for each molecule.

CHAPTER 2

Lab 2 - Molecular transistor

2.1

Two thiophene molecules - double binding

The goal of this exercise is to calculate the I-V caractheristic and the transmission
spectrum of 2 thiolated molecules of thiophene, bonded in parallel on both sides to a
gold nanogap.

2.1.1

Molecule Preparation

Open Builder, click Add / From File / the optimized molecule (1TT-S.py or
opt-lab1.nc). Delete Hydrogen atoms near to left and right sulfur atom.
In the Builder window, CTRL+A / Coordinates Tools / Translate / Copy enable
/ x=3, y=0, z=0 / Apply. You should now see two identical molecules in parallel.
Figure 2.1 shows the result of this step.

Figure 2.1: Two molecules in parallel

2.1.2

Molecular Junction Building

Repeat the tutorial of section 1.6.5, the result is shown in Figure 2.2.

17

Molecular Electronics

18

Figure 2.2: Two Thiophenes in parallel bonded to the gold extremities

2.1.3

Script Generator

In the Molecular Device Builder window compose: click on the arrow located
in the lower right hand corner of the window / Script Generator. Double click
on New Calculator / New Calculator. The list of calculator settings is to define
the parameters and the methods of the calculation: Calculators / Basis set/exchange correlation / Single zeta all over / OK. This point is equivalent to the
Script Generator point of the previous exercise, figures 1.18 and 1.19. After the
completion of simulation, save the transmission file in .txt formate.
This will take some time, in the mean while you can find the I-V characteristics of
molecular systems that you have studied in previous lab using TAMTAMS.

2.2

TAMTAMS

The TAMTAMS Molecular analysis can estimate very well non equilibrium electron
transport characteristics of molecular FET with very low computational complexity.
The transmission spectrum, which we calculated in the previous lab for different molecular system, will be now used to find the I-V characteristics of molecular system. In
this exercise we will explain how to import the transmission spectrum file in TAMTAMS and find IV of the molecular system for a bias voltage comprise between 2V
and +2V .
First login to TAMTAMS web (http://msyslabserver.polito.it/test/login.php)
After login, click Start Analysis then Extra Analysis and then I-V evaluation of molecular FET.
Importing Transmission Spectrum file to TAMTAMS: Before importing the transmission file ( for example 0bias-lab1.txt), first delete all the header/ footer from
the file, leave data only and save it. Import the file to TAMTAMS and click next.
You will get information of the input file, click next.
set the parameter according to Figure.2.4 and Perform all The following three
different type of I-V analysis and note the difference between them.

Molecular Electronics

19

Figure 2.3: Information of Transmission file uploaded.

discrete levels (DL): In Discrete Level modelling, the molecular enegy levels
i.e. HOMO and LUMO are treated as discrete. Broadening of molecular
energy levels due to coupling is ignored. In this model, the molecular conduction is mainly influenced by HOMO or LUMO, coupling to electrode
(1,2 )and charging energy. In this case you will get a step like I-V characteristics of molecular FET.
Density of State i.e including broading of the level (DOS): When a molecule
is coupled with electrodes, the energy level (HOMO and LUMO) broadens.
In order to take this into account, the discrete levels are replaced with
Lorentzian Density of State. In this case, due to broadening of molecular
levels, you will get current even at small biased voltages.
Transmission Spectrum (TQ): In real molecule, we have multiple energy
level that are broadened and overlap. In order to take this into account
NEGF formalism is used to find the realistic transmission spectrum. In
previous exercises you have used VNL, to find the transmission spectrum of
molecular system at equilibrium . Now using this model you will find the
I-V characteristics of molecular system at non-equilibrium. Compare the
result of this model with the result of Density of State (DOS).
To find the effect of charging energy transport properties of molecular system,
change the Self Consistent Field energy to 1 and again perform the simulations
for all three type of I-V analysis.
Repeat simulation for all other molecules.

2.3

Two thiophene molecules - single binding

In this exercise we will study another case in which two molecules are bonded in parallel
on one side of the gold electrode.
Start from importing single thiophene molecule to builder window.

Molecular Electronics

20

Figure 2.4: Parameters setting of Thiophene bonded to gold nanogap through Sulfur
atoms
In the Builder window, CTRL+A / Coordinates Tools / Translate / Copy enable
/ x=3.0, y=0.0, z=3.0 / Apply. You should now see the molecule as shown in
Figure 2.5.

Figure 2.5: Two molecules in parallel and shifted in Z direction

For Molecular Junction Building, Script Generator of the Molecular Junction and
Transmission Function, repeat the tutorial of section 1.6.5 to 1.6.8. The result of
molecular junction is shown in Figure 2.6.
Finally find the I-V characteristics of the molecular system using TAMTAMS
and compare the result with the 2 thiophene molecule bonded on both side to
electrodes.

Molecular Electronics

21

Figure 2.6: Two Thiophenes in parallel bonded in single side to the gold electrodes