1

1. INTRODUCTION

Carbon nanotubes attracted a great interest due to their unique mechanical, electrical
and chemical properties since their discovery. They are shown as one of the most
promising material for applications in materials science and medicinal chemistry. Carbon
nanotubes are arrangements of carbon hexagons that are formed into tiny tubes having
diameter range from a few angstroms to tens of nanometers and can have lengths of up to
several centimeters. As developing the nanotechnology, carbon nanotubes are one of the
most famous materials used as prototype of confinement system to investigate by means of
molecular dynamics simulation methods the adsorption properties of H2, H2O and CO2.
CO2 is known as the most important fluid in biological, geological and chemical systems
after water. Because it has an important role in cellular respiration, it is utilized by plants
during photosynthesis, it can be produced by lots of human activities and it is one of the
most important green house gases. Therefore, molecular simulations of confined CO2 in
carbon nanotubes are necessary to improve the solutions for these problems.

In this study, the aim was to analyze the behavior of CO 2 molecules confined in
single walled carbon nanotubes (SWNTs). To be able to accomplish this purpose, three
different simulations groups were prepared. In the first group four periodic computational
boxes were filled with CO2 and four SWNTs in different sizes were placed in those boxes
separately. In the second group, effect of SWNT amount on CO 2 behavior was observed by
running simulations with two and four SWNTs in same size. Finally, as a third group,
behavior of supercritical CO2 was examined with one SWNT inside the box.

This report contains theory, molecular dynamics simulations, results and discussion
parts. In theory, structures, properties production techniques, of carbon nanotubes and
molecular dynamics approach was explained in detail. Molecular dynamics simulation
methods and parameters used and reasons were described in the molecular dynamics
simulations part. Corresponding results, relevant figures, comparisons and related
comments among the simulation groups were represented in the results and discussion part.
 2

2. THEORY

2.1. CARBON NANOTUBES

Carbon can form diamond which is known as one of the hardest materials and it can
also form one of the softest materials, graphite. In graphite, the carbon atoms are only
bonded in two dimensions. The carbon atoms form layered sheets of hexagons and those
layers may slip off one another easily because there are no bonds between the layers [1].

Figure 2.1. Representation of layered graphite sheets [1]

The properties of each material change according to arrangement of atoms. The

carbon atoms which form tiny tubes called as carbon nanotubes, and they are twice as
strong as steel but weigh six times less [1]. The first carbon fibers in nanodimensions were
discovered in 1976 by Endo [2] who synthesized carbon filaments of 7 nm in diameter
using a vapor-growth technique. But those filaments were not defined as carbon nanotubes
(CNTs) until Sumio Iijima’s report in 1991 [3] which brought CNTs to the attention of the
scientific community [4]. At the same time, researchers at the Institute of Chemical
Physics in Moscow also independently discovered carbon nanotubes and nanotube bundles
having a much smaller length-to-diameter ratio. The shape of these nanotubes led the
Russian researchers to call them ‘barrelenes’ [5].
 3

A single-walled carbon nanotube can be visualized as a seamless cylinder formed by

a hexagonal graphite layer (see Figure 2.2.). A SWNT may grow as long as several
microns in length but also, only a few nm in diameter ranging from 0.4 to 3 nm making it a
perfect one-dimensional material [6]. The structure of a carbon nanotube is like a sheet of
graphite rolled up into a tube. Depending on the direction of chirality vector, nanotubes can
be classified as either zigzag, armchair or chiral. Different types of nanotubes have
different properties [1].

A nanotube can also contain multiple cylinders of different diameters nested inside
one another depending on the synthesis procedure. This type is called a multi-wall
nanotube (MWNT) and also known as ‘Russian dolls’. (MWNTs), as shown in Figure 2.2.,
are composed of a concentric arrangement of numerous SWNTs, often capped at their ends
by one half of a fullerene-like molecule. The distance between two layers in MWNTs is
0.34 nm. Multiwalled nanotubes can reach diameters of up to 200 nm. Other varieties of
nanotubes include ropes, bundles and arrays. [6]

Figure 2.2. Schematic representation of SWNT and MWNT [7]

2.2. THE STRUCTURE OF CARBON NANOTUBES

A carbon nanotube is based on a two-dimensional graphene sheet. The chiral vector

is defined on the hexagonal lattice as:

C h = naˆ1 + maˆ 2 (2.1)

 4

where â1 and â2 are unit vectors, and n and m are integers. The chiral angle, θ, is measured
relative to the direction defined by â1. This diagram has been constructed for (n, m) = (4,
2), and the unit cell of this nanotube is bounded by OAB'B. To form the nanotube, it can be
imagined that this cell is rolled up so that O meets A and B meets B', and the two ends are
capped with half of a fullerene molecule. Different types of carbon nanotubes have
different values of n and m [5].

Figure 2.3. a) Schematic of 2-D graphene sheet illustrating lattice vectors a1 and a2.
b) Possible vectors specified by the pairs of integers (n,m) for carbon nanotubes including
zigzag, armchair and chiral tubules [5]

Zigzag nanotubes correspond to (n, 0) or (0, m) and have a chiral angle of 0°,
armchair nanotubes have (n, n) and a chiral angle of 30°, while chiral nanotubes have
 5

general (n, m) values and a chiral angle of between 0° and 30°. According the theory,
nanotubes can either be metallic (green circles) or semiconducting (blue circles) [5]. In
Cartesian coordinates;

3a a 3
a1 = x+ y
2 2 (2.2)

3a a 3
a2 = x− y (2.3)
2 2

Where a is the nearest-neighbour carbon-carbon spacing of about 1.4Å, and x and y

are unit vectors in the x- and y-directions respectively [8].

Figure 2.4. Structure of armchair, zigzag and chiral carbon nanotubes [9]

The properties of nanotubes are determined by their diameter and chiral angle, both
of which depend on n and m. The diameter, dt, is simply the length of the chiral vector
divided by 0.25, and it was found that;

 3
dt =  (
 π ac −c m + nm + n
2 2
)
1/ 2
(2.4)
 
 6

where ac-c is the distance between neighboring carbon atoms in the flat sheet. In turn, the
chiral angle is given by;

 3n 
θ = tan −1
  (2.5)
 2m + n 
 

A SWNT is considered metallic if the value n − m is divisible by three. Otherwise,

the nanotube is semiconducting. Consequently, when tubes are formed with random values
of n and m, it would be expected that two-thirds of nanotubes would be semi-conducting,
while the other third would be metallic, which happens to be the case [10].

The average diameter of a SWNT is 1.2 nm. However, nanotubes can vary in size,
and they aren't always perfectly cylindrical. The larger nanotubes, such as a (20, 20) tube,
tend to bend under their own weight. The carbon bond length was first determined to be
1.42 Å [11] and later confirmed in 1998 [12]. The C-C tight bonding overlap energy is in
the order of 2.5 eV [12, 13].

2.3. PROPERTIES OF CARBON NANOTUBES

After the discovery of carbon nanotubes (CNTs) in 1991 [3], the world envisioned a
rapid growth of nanotube research. Both theoretical and experimental investigations
revealed that the unique structure of nanotubes provide remarkable mechanical, electronic,
and optical properties [6].

Nanotubes have been known to be up to one hundred times as strong as steel and
almost two millimeters long [14] having a hemispherical "cap" at each end of the cylinder.
They are light, flexible, thermally stabile, and are chemically inert and have the ability to
be either metallic or semi-conducting depending on the "twist" of the tube [5].

2.3.1. The Strength of Nanotubes

The carbon nanotube is the strongest and stiffest material known. Theoretically,
nanotubes have a tensile strength of 130-150 GPa. In the lab, individual tubes have been
produced with a tensile strength of up to 63 GPa stronger than diamond, Kevlar, or spider's
 7

silk with a Young's Modulus of over 1000 GPa, these tubes don't bend under the pressure
either [15].

The strength of the nanotube compared to other forms of carbon lies in its chemical
bonds. Nanotubes are composed of sp2 carbon bonds, forming a hexagonal lattice. These
are stronger than the sp3 bonds which form the cubic structure of diamond [15].

It is unknown whether macro scale nanomaterials can be made with the strength of
individual tubes. When nanotubes are combined with polymers they form super-strong
composites making projects like the space elevator closer to reality. However, these
materials still can't match the strength of the individual nanotube [15].

Table 2.1. Comparison of CNT strength: carbon nanotube-enhanced composite formed by

embedding carbon nanotubes in a polymer matrix [15]

Young's Modulus Tensile Strength Density

Material
(GPa) (Gpa) (g/cm3)
SWNT 1054 150 1.4
MWNT 1200 150 2.6
Diamond 600 130 3.5
Kevlar 186 3.6 7.8
Steel 208 1.0 7.8
Wood 16 0.008 0.6

The extraordinary mechanical properties of carbon nanotubes arise from σ bonds

between the carbon atoms. Experimental measurements together with theoretical
calculations show that nanotubes exhibit the highest Young’s modulus (elastic modulus E)
and tensile strength among known materials. The elastic modulus of single walled CNTs
was reported to be can be up to 1.5 TPa [16]. The ultimate strength of CNTs, ranging from
13 to 150 GPa, surpasses that of materials well-known for their high tensile strength, such
as steel and synthetic fibers [17, 18]. Unlike electrical properties, Young’s modulus of
CNTs is independent of tube chirality, although it depends on tube diameter [19].
 8

Figure 2.5. Illustration of the elastic modulus and strength of carbon nanotubes [6] and
common tissue engineering materials: PGA, PLLA, bone, titanium, steel [4]

The elastic response of a nanotube to deformation is also outstanding. Both,

theoretical and experimental studies revealed that CNTs can sustain up to 15 per cent of
tensile strain before fracture. CNTs are shown to be very flexible with a reversible bending
up to angles of 110o and 120o for MWNTs and SWNTs, respectively [20].

The extraordinary mechanical properties of CNTs have met great interest in the
application of nanotubes in tissue engineering. Properties like the high tensile strength and
excellent flexibility give them superiority over popular materials used (PGA, PLLA,
titanium, steel) and make them ideal candidates for the production of lightweight, high-
strength bone materials. For comparison, Figure 2.5., shows the elastic modulus and
strength of CNTs, bone, and several other common materials used in one-tissue
engineering.
 9

Table 2.2. Physical Properties of SWNT [21]

Equilibrium Structure Optical Properties

Average Diameter
1.2-1.4 nm Fundamental Gap
of SWNT's

For (n, m); n-m is divisible by

Distance from 0 eV
3 [Metallic]
opposite Carbon 2.83 Å
Atoms (Line 1) For (n, m); n-m is not divisible
~ 0.5 eV
by 3 [Semi-Conducting]
Analogous Carbon
Atom Separation 2.46 Å Electrical Transport
(Line 2)
Parallel Carbon
Bond Separation 2.45 Å Conductance Quantization n x (12.9 k)-1
(Line 3)
Carbon Bond
1.42 Å
Length (Line 4)
Resistivity 4-Oct-cm
C - C Tight Bonding
~ 2.5 eV
Overlap Energy
Group Symmetry
C5V
(10, 10)
Maximum Current Density 1013 A/m2
Lattice: Bundles of
Triangular Lattice (2D)
Ropes of Nanotubes
Lattice Constant 17 Å
Thermal Conductivity ~ 2000 W/m/K
Lattice Parameter
(10, 10) Armchair 16.78 Å
Phonon Mean Free Path ~ 100 nm
(17, 0) Zigzag 16.52 Å
(12, 6) Chiral 16.52 Å
Relaxation Time ~ 10-11 s
Density
(10, 10) Armchair 1.33 g/cm3 Elastic Behavior
(17, 0) Zigzag 1.34 g/cm3
Young's Modulus (SWNT) ~ 1 TPa
(12, 6) Chiral 1.40 g/cm3
Interlayer Spacing
Young's Modulus (MWNT) 1.28 TPa
(n, n) Armchair 3.38 Å

(n, 0) Zigzag 3.41 Å

Maximum Tensile Strength ~30 GPa
(2n, n) Chiral 3.39 Å

2.3.2. Electrical Properties of Carbon Nanotubes

The electronic structure of carbon nanotubes is determined by their chirality and


diameter, or, in other words, by their chiral vector C h . CNTs are conductive if the
integers are: n = m (armchair) and n − m = 3i (where i is an integer). In all other cases,
they are semiconducting. The energy band gap Eg for semiconducting nanotubes is given
by [22]:
 10

2γ o a c −c
Eg = (2.6)
d

where, γ 0 = 2.45 eV is the nearest-neighbour overlap integral [14], a c −c the nearest

neighbor C-C distance (~ 1.42 Å), and d is the diameter of the nanotube. Thus, the Eg of a
1 nm wide semiconducting tube is roughly 0.7 eV to 0.9 eV [22]. It has been
experimentally verified that SWNTs and MWNTs behave like quantum wires because of
the confinement effect on the tube circumference [4]. The conductance for a carbon
nanotube is given by [2]:

 e2 
G = Go M =  2 M (2.7)
 h 

where, Go = ( 2e2 h ) = (12 .9 kΩ) is the quantum unit of conductance. M is the apparent
−1

number of conducting channels including electron-electron coupling and intertube

coupling effects in addition to intrinsic channels (M equals 2 for perfect SWNTs), e is the
electron charge, and h is Planck’s constant.

2.3.3. Chemical Properties of Carbon Nanotubes

Small radius, large specific surfaces, and σ - π rehybridization make carbon

nanotubes very attractive for chemical and biological applications because of their strong
sensitivity to chemical or environmental interactions [22]. The chemical functionalization
of carbon nanotubes is a very promising target since it can improve solubility,
processibility, and moreover allows the exceptional properties of carbon nanotubes to be
combined with those of other types of materials. Up to now, several methods for the
functionalization of CNTs have been developed. These methods include covalent
functionalization of sidewalls, noncovalent exohedral functionalization (for example with
surfactants and polymers), endohedral fictionalization, and defect functionalization as
shown in Figure 2.6. Chemical groups on CNTs can serve as anchor groups for further
fictionalization, e.g. with biological and bio-active species such as proteins or nucleic acids
[23, 24]. This bioconjugation is especially attractive for biomedical applications of carbon
nanotubes.
 11

Figure 2.6. Various functionalizations of carbon nanotubes: (A) covalentsidewall

functionalization, (B) defect-group functionalization, (C) noncovalent exohedral
functionalization with polymers, (D) endohedral functionalization with, for example, C60,
(E) noncovalent exohedral functionalization with surfactants [4]

2.4. PRODUCTION OF CARBON NANOTUBES

Carbon nanotubes are generally produced by three main techniques, arc discharge,
laser ablation and chemical vapour deposition. In arc discharge, a vapour is created by an
arc discharge between two carbon electrodes with or without catalyst. Nanotubes self-
assemble from the resulting carbon vapour. In the laser ablation technique, a high-power
laser beam impinges on a volume of carbon - containing feedstock gas (methane or carbon
monoxide). At the moment, laser ablation produces a small amount of clean nanotubes,
whereas arc discharge methods generally produce large quantities of impure material. In
general, chemical vapour deposition (CVD) results in MWNTs or poor quality SWNTs.
The SWNTs produced with CVD have a large diameter range, which can be poorly
controlled. But on the other hand, this method is very easy to scale up, what favors
commercial production [25].
 12

2.4.1. Growth Mechanism

The way in which nanotubes are formed is not exactly known. The growth
mechanism is still a subject of controversy, and more than one mechanism might be
operative during the formation of CNTs. One of the mechanisms consists out of three
steps. First a precursor to the formation of nanotubes and fullerenes, C 2, is formed on the
surface of the metal catalyst particle. From this metastable carbide particle, a rodlike
carbon is formed rapidly. Secondly there is a slow graphitisation of its wall. This
mechanism is based on in-situ TEM observations [26].

The exact atmospheric conditions depend on the technique used, later on; these will
be explained for each technique as they are specific for a technique. The actual growth of
the nanotube seems to be the same for all techniques mentioned.

Figure 2.7. Visualization of a possible carbon nanotube growth mechanism. [25]

There are several theories on the exact growth mechanism for nanotubes. One theory
[27] postulates that metal catalyst particles are floating or are supported on graphite or
another substrate. It presumes that the catalyst particles are spherical or pear-shaped, in
which case the deposition will take place on only one half of the surface (this is the lower
curvature side for the pear shaped particles). The carbon diffuses along the concentration
gradient and precipitates on the opposite half, around and below the bisecting diameter.
However, it does not precipitate from the apex of the hemisphere, which accounts for the
hollow core that is characteristic of these filaments. For supported metals, filaments can
 13

form either by "extrusion (also known as base growth)" in which the nanotube grows
upwards from the metal particles that remain attached to the substrate, or the particles
detach and move at the head of the growing nanotube, labeled "tip-growth". Depending on
the size of the catalyst particles, SWNT or MWNT are grown. In arc discharge, if no
catalyst is present in the graphite, MWNT will be grown on the C 2-particles that are
formed in the plasma. [25]

2.4.2. Arc Discharge Method

The carbon arc discharge method, initially used for producing C60 fullerenes, is the
most common and perhaps easiest way to produce carbon nanotubes as it is rather simple
to undertake. However, it is a technique that produces a mixture of components and
requires separating nanotubes from the soot and the catalytic metals present in the crude
product.

This method creates nanotubes through arc-vaporization of two carbon rods placed
end to end, separated by approximately 1mm, in an enclosure that is usually filled with
inert gas (helium, argon) at low pressure (between 50 and 700 mbar). Recent investigations
have shown that it is also possible to create nanotubes with the arc method in liquid
nitrogen [28]. A direct current of 50 to 100 Å driven by approximately 20 V creates a high
temperature discharge between the two electrodes. The discharge vaporizes one of the
carbon rods and forms a small rod shaped deposit on the other rod. Producing nanotubes in
high yield depends on the uniformity of the plasma arc and the temperature of the deposit
form on the carbon electrode [25].

Insight in the growth mechanism is increasing and measurements have shown that
different diameter distributions have been found depending on the mixture of helium and
argon. These mixtures have different diffusions coefficients and thermal conductivities.
These properties affect the speed with which the carbon and catalyst molecules diffuse and
cool, which in turn influence nanotube diameter in the arc process. This implies that single-
layer tubules nucleate and grow on metal particles in different sizes depending on the
quenching rate in the plasma and it suggests that temperature and carbon and metal catalyst
densities affect the diameter distribution of nanotubes [25].
 14

Depending on the exact technique, it is possible to selectively grow SWNTs or

MWNTs, which is shown in Figure 2.8. Two distinct methods of synthesis can be
performed with the arc discharge apparatus.

Figure 2.8. Experimental setup of an arc discharge apparatus

2.4.3. SWNT versus MWNT

The condensates obtained by laser ablation are contaminated with carbon nanotubes
and carbon nanoparticles. In the case of pure graphite electrodes, MWNTs would be
synthesized, but uniform SWNTs could be synthesized if a mixture of graphite with Co,
Ni, Fe or Y was used instead of pure graphite. SWNTs synthesized this way exist as
'ropes', see Figure 2.9. Laser vaporization results in a higher yield for SWNT synthesis and
the nanotubes have better properties and a narrower size distribution than SWNTs
produced by arc-discharge. Nanotubes produced by laser ablation are purer (up to about 90
per cent purity) than those produced in the arc discharge process. The Ni/Y mixture
catalyst (Ni/Y is 4.2/1) gave the best yield [25].

The size of the SWNTs ranges from 1-2 nm, for example the Ni/Co catalyst with a
pulsed laser at 1470 °C gives SWNTs with a diameter of 1.3-1.4 nm [30]. In case of a
continuous laser at 1200 °C and Ni/Y catalyst (Ni/Y is 2:0.5 at. per cent), SWNTs with an
average diameter of 1.4 nm were formed with 20-30 per cent yield, as shown Figure 2.9.
 15

Figure 2.9. TEM images of a bundle of SWNTs catalyzed by Ni/Y (2:0.5 at. per cent)
mixture, produced with a continuous laser [29]

Table 2.3. A summary of the major production methods and their efficiency [24]

Method Arc discharge method Chemical vapor deposition Laser ablation (vaporization)
Ebbesen and Ajayan, Endo, Shinshu University,
Who Smalley, Rice, 1995 [32]
NEC, Japan 1992 [30] Nagano, Japan [31]

Connect two graphite Blast graphite with intense laser

Place substrate in oven, heat to
rods to a power supply, pulses; use the laser pulses rather
600 oC, and slowly add a
place them a few than electricity to generate carbon
carbon-bearing gas such as
How millimetres apart, and gas from which the NTs form; try
methane. As gas decomposes it
throw the switch. At 100 various conditions until hit on one
frees up carbon atoms, which
amps, carbon vaporises that produces prodigious amounts
recombine in the form of NTs
and forms a hot plasma. of SWNTs

Typical
30 to 90 20 to 100 Up to 70
yield (%)
Long bundles of tubes (5-20
Short tubes with Long tubes with diameters
SWNT microns), with individual diameter
diameters of 0.6-1.4 nm ranging from 0.6-4 nm
from 1-2 nm.
Short tubes with inner
Not very much interest in this
diameter of 1-3 nm and Long tubes with diameter
MWNT technique, as it is too expensive,
outer diameter of ranging from 10-240 nm
but MWNT synthesis is possible.
approximately 10 nm
SWNTs have few
structural defects; Easiest to scale up to industrial
Primarily SWNTs, with good
MWNTs without production; long length, simple
Pro diameter control and few defects.
catalyst, not too process, SWNT diameter
The reaction product is quite pure.
expensive, open air controllable, quite pure
synthesis possible
Tubes tend to be short Costly technique, because it
with random sizes and NTs are usually MWNTs and requires expensive lasers and high
Con
directions; often needs a often riddled with defects power requirement, but is
lot of purification improving
 16

2.5. SUPERCRITICAL FLUIDS

Supercritical fluids are highly compressed gases which combine properties of gases
and liquids in an intriguing manner. Fluids such as supercritical xenon, ethane and carbon
dioxide offer a range of unusual chemical possibilities in both synthetic and analytical
chemistry. The use of supercritical CO2 (scCO2) is explored as an environmentally
acceptable alternative to conventional solvents for reaction chemistry, so called "Clean
Technology". In addition, supercritical fluids can lead to reactions which are difficult or
even impossible to achieve in conventional solvents [34].

The definition of a supercritical fluid usually begins with a phase diagram, which
defines the critical temperature and pressure of a substance. (CO2 ; Tc = 31.1 °C, Pc = 73.8
bar) [35].

2.6. MOLECULAR DYNAMICS

Understanding the properties of assemblies of molecules in terms of their structure

and the microscopic interactions between them serves as a complement to conventional
experiments, enabling us to learn something new, something that cannot be found out in
other ways. The two main families of simulation technique are molecular dynamics (MD)
and Monte Carlo (MC); additionally, there is a whole range of hybrid techniques which
combine features from both. The obvious advantage of MD over MC is that it gives a route
to dynamical properties of the system: transport coefficients, time-dependent responses to
perturbations, rheological properties and spectra [36].

Computer simulations act as a bridge (see Figure 2.10.) between microscopic length
and time scales and the macroscopic world of the laboratory. It can be provided a guess at
the interactions between molecules, and obtain exact predictions of bulk properties. At the
same time, the hidden detail behind bulk measurements can be revealed. Simulations act as
a bridge in another sense, between theory and experiment. It may be tested a theory by
conducting a simulation using the same model and the model may be tested by comparing
with experimental results. Also, simulations on the computer that are difficult or
impossible in the laboratory (for example, working at extremes of temperature or pressure)
 17

may be carried out. Aim of so-called ab initio molecular dynamics is to reduce the amount
of fitting and guesswork in this process to a minimum. When it comes to aims of this kind,
it is not necessary to have a perfectly realistic molecular model; one that contains the
essential physics may be quite suitable [36].

Figure 2.10. Simulations as a bridge between (a) microscopic and macroscopic. (b) Theory
and experiment [36]

Molecular dynamics simulation consists of the numerical, step-by-step, solution of

the classical equations of motion, which for a simple atomic system may be written:

∂
mi ri = f i = − U (2.8)
∂ri

For this purpose it is need to be able to calculate the forces fi acting on the atoms, and
these are usually derived from a potential energy U(rN), where rN = (r1, r2,…,rN) represents
the complete set of 3N atomic coordinates [36].

Molecular simulations are almost invariably conducted in the context of an

ensemble. An ensemble can be regarded as an imaginary collection of a very large number
of systems in different quantum states with common microscopic attributes. For instance,
each system of the ensemble must have the same temperature, pressure and number of
molecules as the real system it represents. The choice of ensemble determines which
thermodynamic properties can be evaluated and it also governs the overall simulation
 18

algorithms. MC and MD algorithms for a specified ensemble are very different, reflecting
fundamental differences in the two simulation methods [37].

Typical uses of molecular dynamics include searching the conformational space of

alternative amino acid side chains in specific mutation studies, identifying likely
conformational states for highly flexible polymers or for flexible regions of
macromolecules such as protein loops, calculating free energies binding including
solvation and entropy effects, probing the locations, conformations and motions of
molecules on catalyst surfaces and running diffusion calculations [37].

2.6.1. Energy Minimization

A general minimization process contains two steps as energy evaluation and

conformation adjustment. Minimization of a model is also done in two steps. First, the
energy expression (an equation describing the energy of the system as a function of its
coordinates) must be defined and evaluated for a given conformation. Energy expressions
may be defined that include external restraining terms to tend the minimization, in addition
to the energy terms. Next, the conformation is adjusted to lower the value of the energy
expression. A minimum may be found after one adjustment or may require many
thousands of iterations, depending on the nature of the algorithm, the form of the energy
expression, and the size of the model. The efficiency of the minimization is therefore
judged by both the time needed to evaluate the energy expression and the number of
structural adjustments (iterations) needed to converge to the minimum [38].

Energy minimization is used for optimizing initial geometries of models constructed

in a molecular modeling program such as Cerius2 [39] or Insight®. It repairs poor
geometries occurring at splice points during homology building of protein structures and
maps the energy barriers for geometric distortions and conformational transitions using
torsion forcing to obtain Ramachandran type contour plots for protein or RIS statistical
weights for polymers. It also evaluates whether a molecule can adopt a template
conformation consistent with a pharmacophoric or catalytic site model which is known as
template forcing [38].
2.6.2. Simple Thermodynamic Averages
 19

Energy: The total energy (E) or Hamiltonian (H) of the ensemble can be obtained
from the ensemble averages of kinetic (Ekin) and potential energies (Epot).

E = E kin + E pot (2.9)

The kinetic energy can be evaluated from the individual momenta of the particles and
the potential energy is the sum of the interparticle interactions which are usually calculated
by assuming a particular intermolecular function.

Temperature: The temperature can be obtained from the virial theorem. In terms of
generalized momenta (pk), the theorem can be expressed as:

∂H
pk = kT (2.10)
∂p k

For N atoms, each with three degrees of freedom, the following relation can be
obtained.
2 E kin
T = (2.11)
3 Nk

Alternatively, it can be considered that T to be the average of instantaneous

temperature contributions (t) [37].

2 E kin
t= (2.12)
3 Nk

2.6.3. Canonical (NVT) Ensemble

For generating a canonical ensemble, the number of particles, volume and

temperature should be constant and there are not so much different options for that. The
simplest method to make temperature constant includes velocity scaling or heat-bath
coupling. Alternatively, thermostats of Andersen [40], Nosé [41], Hoover [42] or a general
constraint approach can be used. These latter alternatives involve modifying the equation
of motion [37].
 20

Andersen [40] proposed an alternative to velocity scaling which combines molecular

dynamics with stochastic processes and guarantees a canonical distribution. At constant
temperature, the energy of a system of N particles must fluctuate. This fluctuation can be
introduced by changing the kinetic energy via periodic stochastic collisions. At the outset
of the simulation, the temperature (T) and the frequency (ν) of stochastic collisions are
specified. At any time interval (Δt), the probability that a particular particle is involved in a
stochastic collisions is νΔt [37]. A suitable value of ν is:

νc
ν = (2.13)
N23

where νc is the collision frequency.

During the simulation, random numbers can be used to determine which particles
undergo stochastic collision at any small time interval. The simulation proceeds as follows.
Initial values of positions and momenta are chosen and the equations of motion are
integrated in the normal way until the time is reached for the first stochastic collision. The
momentum of the particle chosen for the stochastic collision is chosen randomly from a
Boltzmann distribution at temperature T. The collision does not affect any of the other
particles and the Hamiltonian equations for the entire particles are integrated until the next
stochastic collision occurs. The process is then repeated. [37]

2.7. MOLECULAR INTERACTIONS

A molecular dynamics simulation determines the individual forces experienced by

each molecule. This force is used to determine new molecular coordinates in accordance
with the equations of motion and evaluating the effect of molecular interaction is the most
computational time consuming step and as such, it governs the order of the overall
algorithms.
In principle, for a system of N molecules, the order of the algorithm scales as Nm
where m is the number of interactions that are included. If only the distinguishable
interactions are considered, N ( N −1) / 2 calculations are required for each configuration.
 21

Molecular forces can be characterized as either short-range or long-range and

different techniques are required to simulate both types of properties. A long-range force is
defined as one which falls off no faster than r-d where d is the dimensionality of the system.
Typically, ion-ion and dipole-dipole potentials are proportional to r-1 and r-3, respectively.
Dispersion and repulsion are examples of short-range forces.

Many computation-saving devices can be employed to calculate short-range

interactions such as periodic boundary conditions and neighboring lists but, calculating
long-range interaction requires special methods such as Ewald sum, reaction field, and
particle-mesh methods, because the effect of long range interaction extends well past half
the length of the simulation box [37].

2.7.1. Non-bonded Interactions

The part of the potential energy Unon-bonded representing non-bonded interactions

between atoms is traditionally split into 1-body, 2-body, 3-body . . . terms:

U non −bonded (r N ) = ∑u ( ri ) + ∑∑ν (ri , r j ) + ... (2.14)

i i j >i

The u(r) term represents an externally applied potential field or the effects of the
container walls; it is usually dropped for fully periodic simulations of bulk systems. Also,
it is usual to concentrate on the pair potential v (ri; rj) = v (rij) and neglect three-body (and
higher order) interactions. There is an extensive literature on the way these potentials are
determined experimentally, or modeled theoretically [43-46].

Differentiable pair-potentials (although discontinuous potentials such as hard spheres

and spheroids have also played a role). The Lennard-Jones potential is the most commonly
used form:
 σ 
12
σ 
6

ν LJ ( r ) = 4ε   −    (2.15)
 r  r 
 22

With two parameters: σ, the diameter, and ε, the well depth. This potential was used,
for instance, in the earliest studies of the properties of liquid argon [47-48]. For
applications in which attractive interactions are of less concern than the excluded volume
effects which dictate molecular packing, the potential may be truncated at the position of
its minimum, and shifted upwards to give what is usually termed the WCA model [49]. If
electrostatic charges are present, we added the appropriate Coulomb potentials:

Q1Q2
ν Coulomb ( r ) = (2.16)
4π εo r

where Q1 and Q2 are the charges and ε0 is the permittivity of free space.

2.7.2. Bonded interactions

For molecular systems, it is simply built the molecules out of site-site potentials of
the form of Equation 2.15 or similar. Typically, a single-molecule quantum-chemical
calculation may be used to estimate the electron density throughout the molecule, which
may then be modeled by a distribution of partial charges via Equation 2.16, or more
accurately by a distribution of electrostatic multipoles [46, 50]. For molecules it should
also be considered the intramolecular bonding interactions. The simplest molecular model
includes terms of the following kind:

(2.17a)

∑ ki j( ri j − re q) 2
1 r
U i n t r a mu ol al =re c
2bo n d s

+ ∑ k iθ j k(θ i j k− θ e q)
1
2b e n d
2
(2.17b)
a ng les

∑ ∑ kiφj,mk l(1 + c o( ms φ i j k −l γ m )
1
+
2t o r s io n
a ng les

(2.17c)
 23

Figure 2.11. Geometry of a simple chain molecule, illustrating the definition of interatomic
distance r23, bend angle θ234, and torsion angle ϕ1234 [36]

Equation 2.17a shows the interaction between pairs of bonded atoms which can be
defined as bond stretching. Equation 2.17b is for angle bending which is deviation of
angles from the reference angle θ0 and it is calculated by the total value of angle between
three atoms 2-3-4 which illustrated in Figure 2.11. Another force that should be taken
account as bonding interactions is torsion terms which define the energy change due to
bond rotations. Equation 2.17c shows the calculation method of torsion angles and ω is the
torsion angle, Vn is the barrier height, γ is phase factor and n is the number of minimum
points in the function as the bond is rotated through 360o [36]. Sum of both intermolecular
and intramolecular interactions gives the total potential energy with respect to position.

V (r N
)=1
2
∑
k (r r
ij i
j −
req ) 2

b
ond
s

1
+ ∑
2 b
end
k iθ
j
k ( θ−
θ)
ij
k e
q
2

a
ngl
es

1
+ ∑ k ijφ
∑ k
l
,m
(
1+c
os (mφ
i
jkl −m γ )) (2.18)
2 to
rs
ion
a
ngl
es

ε σ σ
  ij
1
2
 ij  6
Q Q 
  
 4π
εr
N N

∑ ∑     i j
+ 4 − + 
  rij  rij 
i=1 j=
i+1
 
    o i
j


2.8. PERIODIC BOUNDARY CONDITIONS

Small sample size means that, unless surface effects are of particular interest,
periodic boundary conditions need to be used. Consider 1,000 atoms arranged in a
10 ×10 ×10 cube. Nearly half the atoms are on the outer faces, and these will have a large
 24

effect on the measured properties. Even for 10 6 = 100 3 atoms, the surface atoms amount to
6 per cent of the total, which is still nontrivial. Surrounding the cube with replicas of itself
takes care of this problem. Provided the potential range is not too long, it can be adopted
the minimum image convention that each atom interacts with the nearest atom or image in
the periodic array. In the course of the simulation, if an atom leaves the basic simulation
box, attention can be switched to the incoming image. As a particle moves out of the
simulation box, an image particle moves in to replace it. In calculating particle interactions
within the cutoff range, both real and image neighbors are included. This is shown in
Figure 2.12. It is important to bear in mind the imposed artificial periodicity when
considering properties which are influenced by long-range correlations. Special attention
must be paid to the case where the potential range is not short: for example for charged and
dipolar systems [36].

Figure 2.12. Representation of periodic boundary conditions [36]

2.9. FORCE FIELDS

The force field contains the necessary building blocks for the calculations of energy
and force:
 25

• A list of atom types.

• A list of atomic charges (if not included in the atom-type information).
• Atom-typing rules.
• Functional forms for the components of the energy expression.
• Parameters for the function terms.
• For some force fields, rules for generating parameters that have not been explicitly
defined.
• For some force fields, a defined way of assigning functional forms and parameters.

This total package for the empirical fit to the potential energy surface is the force
field [32]. All the CFF force fields (CFF91, CFF, PCFF, COMPASS) have the same
functional form, differing mainly in the range of functional groups to which they were
parameterized (and therefore, having slightly different parameter values). These
differences can be examined by using the force field editing capabilities of Cerius2 [39]
and Insight® [38] or in the force field files. Atom equivalences for assignment of
parameters to atom types may also differ; as may some combination rules for non bond
terms. Both anharmonic diagonal terms and many cross terms are necessary for a good fit
to a variety of structures and relative energies, as well as to vibrational frequencies [38].

PCFF was developed based on CFF91 and is intended for application to polymers
and organic materials. It is useful for polycarbonates, melamine resins, polysaccharides,
other polymers, organic and inorganic materials, about 20 inorganic metals, as well as for
carbohydrates, lipids, and nucleic acids and also cohesive energies, mechanical properties,
compressibilities, heat capacities, elastic constants. It handles electron delocalization in
aromatic rings by means of a charge library rather than bond increments [38].

2.10. BEHAVIOR OF FLUIDS CONFINED IN CARBON NANOTUBES

With the development of high technology and modern research methods, chemical
engineering is intercrossing and co-developing with chemistry, physics, material science
 26

and bi molecular technology and the new technologies in chemical industry include such
complex materials as polymer and electrolyte, such complex conditions as critical and
supercritical, and such complex phenomenon as interface, membrane solution. To achieve
the vision of completely automated product and process design in chemical industry, the
properties of the materials, the proper theoretical models and the mechanism of the
phenomena should be accurately obtained. The structural and dynamic properties of non-
scale confined fluids are one of the current research focuses, because they are closely
related with ion channels in life science, membrane separation in new style chemical
process and mesoporous catalyst synthesis in high-qualified materials manufacture [51].

As developing the nanotechnology, carbon nanotubes are usually being used as

prototype of confinement system to investigate with molecular simulation methods the
adsorption properties of H2, H2O and CO2. By experiments using relatively high purity
SWNTs, hydrogen storage capacity of about 8 per cent at 80 K and 120 atm was reported
[52]. Alexiadis and Kassinos [53] reported that one of the most striking consequences of
water confinement in CNTs is the complete change of certain of its properties. Because of
the importance of water in biology and medicine, a large number of articles have been
written about the interaction between H2O and CNT under different conditions. After
water, carbon dioxide is probably the most important fluid in biological, geological and
chemical systems. CO2, which is one of the green house gases, is released by human
activity due to fossil fuels usage. Vast majority of the studies is focused on diminishing the
CO2 release by absorbing it on a suitable material. Because of CO2 absorption ability on
CNTs [54], CNTs are very useful especially where CO2 emission level is high.

Due to importance of water and CO2 in each part of life some researches are
performed to compare their behavior by means of interaction with CNTs. Alexiadis and
Kassinos [55] reported that carbon dioxide molecules behave the opposite of water. CNTs
are, in fact, hydrophobic and the density of H2O molecules inside the nanotube is lower
than bulk. By increasing the diameter, however, the density rises and it reaches
asymptotically the value of bulk water. Carbon dioxide, on the other hand, accumulates
spontaneously in the nanotube and at 300 K and 10 bar the concentration can be more than
100 times higher inside than outside the CNT.
 27

3. SIMULATION METHOD

As mentioned in theory part, the CO2 storage ability of CNTs is very important issue
especially in terms of global warming. Since industry is developing almost in each country,
CO2 release increases as well. Therefore some effective solutions are supposed to be
discovered to decrease the effect of CO2 emission. One of the ways proposed is the CO2
confinement in carbon nanotubes, but due to their nanoscale size and packed form, SWNTs
can not be seen alone, making it difficult and expensive to work with in laboratory
conditions. Molecular dynamics simulations were shown to be an alternative option.

In this project the behavior of CO2 confined in SWNTs and influence of size and
amount of single walled carbon nanotubes (SWNTs) on CO2 storage by means of
molecular dynamics was investigated. All molecular dynamics simulations were performed
by XenoView which was developed by Shenogin and Ozisik [57]. This program also
allows visualizing the atomistic simulations at different conditions and by using different
force fields.

Before getting started with the molecular dynamics part, all the systems were energy
minimized after all the molecules were packed into the simulation boxes. During the
preparation of SWNTs around 1×10 4 - 2 ×10 4 iterations of energy minimization were
performed. However, 100-200 iterations with 0 kcal/mol tolerance were sufficient enough
to minimize the energy for SWNT systems with CO2. After the completion of energy
minimization, molecular dynamics parameters were selected. For all the simulations, NVT
ensemble (constant volume and temperature) with Andersen thermostat were used to keep
the temperature of the system constant during the simulation and also periodic boundary
conditions were applied to all simulations. Time step (Δt) was set to 1 fs because above 1
fs, simulations were not stable enough. It was observed with a simulation which time step
was chosen as 2 fs and when the trajectory file was being visualized, system was not
running accurately, bonds lengths between two atoms were increasing and no observation
can be performed for this kind of a simulation. In addition, the reason not to chose time
step below 1 fs, for example 0.5 fs, is to save time. Because, as time step gets smaller, the
duration of simulation increases. Therefore, 1 fs was chosen as time step, instead of 2 fs
 28

and 0.5 fs, to have most accurate results while saving time. Number of steps for simulation
was set from 8 ×10 6 to 25 ×10 6 which makes the total simulation time from 8 ns to 25
ns. That total duration was decided by considering the time required for the simulation to
reach steady. PCFF was chosen as most appropriate force field for our systems and it was
used also to compare the results with previous SWNT/CO2 studies [49] which were
performed with AMBER and CHARMM.

In this work, (6,6), (8,8), (10,10), (16,16) armchair SWNTs were used to investigate
the influence of SWNT size on behavior of CO2 molecules at 300 K. When preparing the
simulations with CO2, in order to prevent the effect of pressure acting on molecules, the
bulk density (ρo) of CO2 molecules was kept constant around 0.04 nm-3. Bulk density is
measured in number of molecules per nm-3. Nanotube diameter d, length L, box size (H x

H x Z), number of CO2 molecules N CO 2 , and ratio between nanotube and box volume
Vb/VCNT are reported in Table 6.1.

Table 6.1 Parameters of first system (CNTs in different sizes)

(n,m) (6,6) (8,8) (10,10) (16,16)

d (Å) 8.0 10.7 13.6 21.4
L (Å) 30.2 39.9 48.4 76.3
NCNT 1 1 1 1
Z (Å) 200 260 300 400
H (Å) 150 160 180 300
N CO 2 189 288 408 1678
Vb/VCNT 2961 1857 1383 1319
ρo (nm-3) 0.042 0.043 0.042 0.046

Also, to figure out the effect of SWNT amount on behavior of CO 2, (10,10) SWNT
simulations were repeated at 300 K with 2 and 4 SWNTs in the box as keeping the number
 29

of CO2 molecules the same. In addition to CO2 and SWNT simulations, the behavior of
super critical CO2 confined in SWNT has also tried to investigate in 2 different box sizes at
400 K while keeping other parameters the same.
 30

4. RESULTS AND DISCUSSION

This study focuses on the fluid behaviors confined in SWNT. CO2 was chosen as
fluid because of the health and environmental impact of CO2 especially as a one of the
most important green house gases, lots of studies are dedicated to improve the decrease
CO2 emission to the atmosphere. The ability of CO2 storage of carbon nanotubes makes
them one of the most promising materials. This study performed to find and optimum
configuration for CO2 storage in SWNT and to observe the behavior of CO2 in the
nanotubes.

Since the experimental studies in this area are very difficult to handle and also very
expensive, molecular dynamics (MD) approach was used in this research. For simulating
our systems, XenoView MD program was used with NVT ensemble (constant volume and
temperature) while using the Andersen thermostat to keep temperature the constant during
the simulation. Periodic boundary conditions were applied to all the simulations as well as
energy minimization. In addition, for all the simulations PCFF was chosen as force field
because its suitability for polymers and carbon related structures.

In this research, there were three main study groups. First simulation group was
prepared to observe the behavior of CO2 molecules when they are confined in nanotubes
which are different in diameter. These simulations were performed with (6,6), (8,8),
(10,10) and (16,16) armchair SWNTs to see the effect of SWNT size to CO2 behavior. The
parameters for this group are shown in Table 6.1. Second simulation group was prepared to
figure out the influence of the number of nanotube to the CO2 behavior. For this purpose,
two additional systems were prepared containing two and four (10,10) SWNTs to compare
with the simulation with single (10,10) nanotube which was performed in the first group.
Parameters for this group was the same with the first single (10,10) nanotube simulation to
make a reliable comparison. In addition to CO2 behavior, super critical CO2 behavior was
also in consideration. Therefore, a third simulation group was prepared including two
boxes in different dimensions and filled with super critical CO2 while putting the same
(10,10) nanotube used in previous simulation groups. The nanotube having same size was
used to be able to make comparison between systems with CO2 and supercritical CO2.
 31

However in this case temperature of the system was chosen as 400 K due to properties of
super critical CO2. For all the simulations 1fs time step and 9Å cut-off radius was chosen
as MD parameters.

4.1 EFFECT OF SWNT SIZE ON CO2 BEHAVIOR

In order to observe the effect of SWNT size to CO2 behavior, 4 different simulations
were run with same bulk density but with different carbon nanotube sizes. As a first
simulation, (6,6) armchair SWNT was put in a simulation box whose dimensions are
shown in Table 6.1. with 189 CO2 molecules. This simulation was run about 15 ns and
after system reached the steady-state, then it was stopped. To investigate the behavior of
CO2 in the system, CO2 density inside carbon nanotube was plotted as a function of time.

Figure 4.1. Change in carbon dioxide density inside a (6,6) SWNT w.r.t. time

As it can be seen from Figure 4.1., at steady state, CO2 density inside SWNT is about
4.5 nm-3. At first sight, four horizontal lines attract the attention in some time intervals
because the density function behavior usually is expected as oscillations. In this case,
however, since nanotube size is very small, CO2 density inside nanotube remains constant
for a little bit long time and this makes those horizontal lines in the graph.
 32

As shown in Figure 4.2, CO2 molecules inside (6,6) SWNT reside as a line, because
of intermolecular forces and some other CO2 molecules surround the external wall of
nanotube because of attractive forces between SWNT and CO2. In other words, (6,6)
nanotube has a diameter of approximately the same size of the C and O atoms. This
circumstance compels the CO2 molecules to align their O-C-O axis parallel to the nanotube
axis. The entrance in the nanotube is thus limited by geometrical consideration. Also, it
shows the carbon atoms tend to remain at the center and the O atoms near the walls. In
general both atoms show a strong interaction with the nanotube and carbon dioxide tends
to lie along the walls forming CO2 tubular layer all around the internal side. It can also be
observed that, cylinder shape of SWNT wasn’t damaged through the simulation because,
this nanotube is not a large one and it does not tend to bend as larger ones like (20,20)
mentioned in Section 2.2.

Figure 4.2 Finalized (6,6) SWNT simulation with CO2

As a second simulation, (8,8) SWNT was put in a simulation box which has
predefined size in Table 6.1. with 288 CO2 molecules. This simulation was run about 12 ns
and after system reached the steady-state, it was stopped. To be able to figure out the
behavior of CO2 in the system, change in CO2 density inside carbon nanotube was shown
with respect to time. In Figure 4.3, it is obvious that, density of CO2 molecules inside (8,8)
CNT increases slowly rather than (6,6) and it takes longer to reach the steady-state.
Because in the (6,6) simulation, there were less atoms than (8,8) and despite all the MD
parameters are the same for both simulation, it is easier and shorter to calculate all forces
between atoms and displacements of molecules.
 33

Figure 4.3. Change in carbon dioxide density inside a (8,8) SWNT w.r.t. time

In the finalized snapshot of (8,8) simulation, it can be observed that intermolecular

forces between CNT and CO2 molecules increases. In this case CO2 molecules inside
nanotube do not appear as a line however, they appear as a ring shape. The reason for this
ring shape structure is, more CO2 molecules are entering into the carbon nanotube rather
than (6,6) and they can not be stay as one line because they have more space so, they
disperse through the nanotube according to inter and intramolecular forces. However, the
main reason for that ring shape structure is CNT-CO2 attraction is stronger than the CO2-
CO2 attraction. Therefore, all these reasons, forces, larger area and attractions etc. make a
ring shape CO2 structure in the nanotube.

In the (8,8) simulation, the CO2 molecules start to surround the external wall of
carbon nanotube more because of increase in intermolecular forces between nanotube and
fluid. And above that accumulation on the external wall of CNT, CO 2 molecules are
observed as moving through an orbit around CNT and the reason for that kind of moving is
long range forces between CO2 and CNT which is smaller than CO2 molecules at the
external wall. The reason for CO2 molecules are not staying perpendicular to the nanotube
is the order parameters.
 34

Figure 4.4. Finalized (8,8) SWNT simulation with CO2

As a third simulation (10,10) SWNT was put in a simulation box whose dimensions
are shown in Table 6.1. with 408 CO2 molecules in it. This simulation was run for 25 ns
and its density profile through the simulation is the following:

Figure 4.5. Change in carbon dioxide density inside a (10,10) SWNT w.r.t. time

The same comparison between (6,6) and (8,8) nanotube can being continued by
adding (10,10). It is so obvious that, the time that last for the (10,10) system to reach the
steady state in terms of CO2 density inside nanotube is longer than the first two simulations
as expected. This is again due to increase in the number of molecules in the system. In the
 35

third simulation a ring shape structure of CO 2 molecules inside nanotube was observed as
well. This time, however, the diameter of the ring shaped structure is larger than the
structure occurred in second simulation which performed with (8,8) SWNT. The reason is
again the CNT-CO2 attraction is stronger than the CO2-CO2 attraction so, CO2 molecules
have tendency to cover the internal walls of nanotube and empty the central part of the
CNT. Because of the diameter of (10,10) nanotube is larger than (8,8), the diameter of ring
shape structure is larger in (10,10) nanotube as well.

Figure 4.6. Finalized (10,10) SWNT simulation with CO2

As a fourth and last simulation to see the influence of SWNT size on CO 2 behavior,
(16,16) SWNT simulation was performed with 1678 CO2 molecules in the simulation box.
This simulation was run for about 10 ns. In the density profile (Figure 4.7.) the actual
steady state time is not clear but it is obvious that system is very close to steady state
because increase in density is very slow rather than the beginning of the simulation. This
system didn’t reach the steady state in terms of density inside (16,16) SWNT because lack
of time. However, still some important discussions can be performed on this simulation.
 36

Figure 4.7. Change in carbon dioxide density inside a (16,16) SWNT w.r.t. time

First of all, the most obvious thing about this simulation which can be seen in Figure
4.8. that it has much more CO2 molecules in it rather than the previous smaller nanotubes
as expected. Since the diameter of this nanotube is larger than others, it has the ability to
store more CO2. Secondly, as mentioned in theory in Section 2.2, this nanotube has bended
under its own weight as expected. At the beginning of the simulation, it has a well cylinder
shape but as simulation runs, it started to bend. The third discussion about this simulation
is the structure of CO2 atoms in the nanotube and also around the external wall of it. It is so
interesting that at the beginning of the simulation, till about 3ns, the CO2 molecules inside
the nanotube are covering the internal wall of the nanotube and creating a ring shape
structure as the previous simulations. After 3-4 ns, however, as the density of CO 2
molecules increases in the nanotube and they start to get together and form separate and
ordered lines in it. Also the CO2 molecules around the external wall of the nanotube they
have the same behavior as the ones inside of it. At the beginning of the simulation till 3-4
ns, they surround the nanotube and after that time, more CO2 molecules accumulate around
nanotube and they have ordered line shape. Both CO2 lines inside and outside of nanotube
were aligned as planes and those planes are located on the same axis.
 37

Figure 4.8. Finalized (16,16) SWNT simulation with CO2

After making individual comparison between the simulations which contains same
bulk density but CNTs in different sizes, a comprehensive discussion can be made between
them.

Figure 4.9. Change in carbon dioxide density inside (6,6), (8,8), (10,10) and (16,16)
SWNT w.r.t. time
 38

Since the aim of this section is to focus on the effect on SWNT size on CO2 behavior,
the density profile of all simulations were plotted in the same graph in Figure 4.9, and it
shows that density of CO2 in (8,8) nanotube is the highest one and in (16,16) nanotube is
the lowest one. This result shows us that for higher density inside CNT, we do not need
very large nanotubes but at the same time it should not be very small. Increase in density
continues till one point in terms of nanotube size, after that point it starts to decrease.

Figure 4.10. Relative carbon dioxide density (density in the nanotube/bulk density) versus
diameter at 5 atm and 300 K

This relation can be seen more clearly in the Figure 4.10. which was plotted by
dividing the density in nanotubes at steady state to their initial value (ρ/ρo). As nanotube
size increases the relative carbon dioxide density (density in the nanotube/ bulk density)
increases as well linearly and after reaching its maximum value it starts to decrease linearly
again but in slower fashion.

4.2 EFFECT OF SWNT AMOUNT ON CO2 BEHAVIOR

After nanotubes size, amount of nanotube is also can be considered as a factor that
affecting the CO2 behavior. For observing this relation, the same initial parameters with
(10,10) nanotube system was used but in this case 2 (10,10) SWNTs were places into the
 39

simulation box just one nanotube instead. Bulk density was kept the same because the
nanotube volumes are very small compared to box volume and this change does not affect
the bulk density a lot. This simulation was run for about 10 ns and their density profiles in
the nanotubes are shown in the Figure 4.11.

Figure 4.11. Change in carbon dioxide density inside two (10,10) SWNT w.r.t. time

In this simulation, it is obvious that none of the carbon nanotubes obstruct the CO 2
catching ability of other. It can be just said that, density increment of first nanotube is
faster than the second one but, at some point very close to 10 ns, they have almost the same
density inside. When compared the first simulation which performed with a single
nanotube in the box with the same dimensions, the steady-state time is almost the same for
both simulations which means making the nanotube number twice in the simulation does
not affect the time that system needs to reach the steady-state. Also, this change doesn’t
affect the steady state density inside nanotubes.

As a third simulation, four (10,10) SWNT was placed into the simulation box again
which having the same parameters with the first two simulations and it was run for about
12 ns. In this simulation there were more atoms than other two so, even if the system could
not reach the steady state, it is obvious that the steady state time for this system will be
longer than the previous simulations. There is no specific increase or decrease in density
for the system having four nanotubes. Density values are not the same for the all nanotubes
 40

in the system but, they are close to each other and towards the end of the simulation they
meet up on almost the same value.

Figure 4.12. Change in carbon dioxide density inside four (10,10) SWNT w.r.t. time

Figure 4.13 Change in density in (10,10) SWNTs for systems having one, two and four
nanotube
4.3. BEHAVIOR OF SUPERCRITICAL CO2 CONFINED IN SWNT
 41

Beside the interaction between CO2 and SWNT, the interaction between supercritical
CO2 and SWNT also attracts a great interest. To observe this interplay, a simulation was
prepared with 531 CO2 molecules which makes the density of CO2 same as the super
critical CO2 (0.469 g/cm3). As the box size (30x30x100) Å is used and (10,10) SWNT was
used as nanotube also temperature is set to 400K as a difference from the previous
simulations because of the properties of supercritical CO2. The box size is not the same
with initial (10,10) nanotube simulations since, filling system with supercritical CO2
molecules means putting much more CO2 molecules than the other simulations which
performed with CO2 and it is a hard process because this procedure requires a very
powerful computer with a lot of time for creating system as well as requiring lots of time
for running the simulation. This simulation was run for approximately 6 ns and the steady
state was observed. The density profile of super critical CO2 molecules in the nanotube is
shown on the Figure 4.14.

Figure 4.14. Change in supercritical carbon dioxide density inside (10,10) SWNT w.r.t.
time with 30x30x100 box size

This system can be compared with the system which was run with 408 CO 2
molecules in a bigger box. While the density inside nanotube is about 10 nm -3 in this
simulation, in the other simulation with just CO2 molecules density is 5.5 nm-3. The
 42

difference here is the bulk density is 5.9 nm-3 and in the nanotube, this density rises to 10
nm -3 which means it was twice. However, in the first simulation with CO2, the bulk density
was 0.042 nm-3 and in the nanotube the density of CO 2 molecules was 5.5 nm-3 which
means the density inside nanotube is almost 100 times higher than bulk density.
As similar with the (16,16) nanotube system, at steady state the super critical CO2
molecules aligned in the box just behind the nanotube. This alignment is so clear in the
Figure 4.15. In this case (10,10) nanotube showed a bending behavior more than (16,16)
and the super critical CO2 molecules inside nanotube did not create a well shaped ring
structure and they didn’t have any aligned position as the molecules outside of the
nanotube as observed in previous (8,8) and (10,10) nanotube simulations.

Figure 4.15. Finalized (10,10) SWNT simulation with supercritical CO2 with 30x30x100
box size

Because of the periodic boundary conditions, when MD has started, as nanotube

moves in the box and since the dimensions of the box is not bigger than nanotube size,
some part of nanotube exiting the box and at the same time it enters to the box from the
other side and this makes the system to be seen as if there are two different nanotubes in
 43

the box. Their interaction can easily be seen in the Figure 4.16. They cause to bend each
other and limiting their movements. Again, due to the periodic boundary conditions, even
if we put one nanotube to the system, in reality the system behaves as if there are other
boxes surrounding our main box and those imaginary boxes also contains nanotubes.
While the MD calculations are being made, surrounding nanotubes are also included; the
nanotube inside the box is obstructed in terms of free movement. Therefore, the same
simulation was repeated in a bigger box to decrease that obstruct effect.

The second simulation with super critical CO2 was prepared in a (60x60x100) Å box
putting 2260 CO2 molecules to make the system filled with super critical CO2. Putting
2260 CO2 molecules to this system makes the bulk density 6.3 nm-3 which is close to the
bulk density of the system with smaller box. This simulation was run for 3 ns and Figure
4.16. shows its density profile with respect to time.

Figure 4. 16. Change in supercritical carbon dioxide density inside (10,10) SWNT w.r.t.
time with 60x60x100 box size

Even if we increased the box size to decrease the interaction between nanotubes due
to periodic boundary conditions, the same response has occurred. In this case nanotubes
(separated forms) are not in succession and they do not cause each other to bend. However,
the rest of the things are the same in terms of structure except steady state time. Density of
 44

supercritical CO2 molecules reached the steady-state value faster than the CO2 molecules.
In this simulation, perfect alignment among CO2 molecules is not seen yet since the system
didn’t run enough as the system with smaller box. But, anyway the tendency of CO2
molecules to align is observed in the Figure 4.17.

Figure 4.17. Finalized (10,10) SWNT simulation with supercritical CO2 with 60x60x100
box size
 45

5. CONCLUSION AND RECOMMENDATIONS

5.1. CONCLUSION

In this project it was aimed to figure out the relation between CO 2 and SWNTs and
the behavior of CO2 molecules confined in SWNTs. To be able to investigate this
association, MD approach was used instead of experimental methods to avoid the
difficulties of handling SWNTs in laboratory conditions and also huge costs which should
be paid for these processes. This study contains three parts: effect of SWNT size to CO2
behavior, effect of number of SWNTs on CO2 behavior and the behavior of super critical
carbon dioxide confined in SWNT.

As a first group, four simulations filled with CO 2 containing SWNTs in different

sizes were prepared while keeping the bulk density around 0.04 nm-3 and parameters of
these systems are shown in Table 6.1. By increasing the diameter, however, CO2 density
inside nanotubes decreases as shown in Figure 4.10. The density profile was not monotonic
at current conditions but it gave a maximum value for the (8,8) nanotube. Beside the
density inside nanotubes, the structure of CO2 molecules inside nanotube was an
interesting point. While CO2 molecules inside (6,6) nanotube residing on an axis as a line,
for (8,8) and (10,10) nanotubes this structure turned in to a ring structure. The reason is the
diameter of (6,6) nanotube is very close to the size of C and O atoms. Therefore CO 2
molecules aligned their O-C-O axis parallel to the nanotube axis. Since the carbon atoms
tend to remain at the center and the O atoms near the walls, in (8,8) and (10,10) nanotubes
CO2 molecules created a hallow cylinder. In (16,16) nanotube simulation, even if the CO 2
molecules created a ring structure at the beginning, towards the end of the simulation they
aligned and made several lines both inside and outside of nanotube which are also parallel
to each other.

As a second group, two and four (10,10) SWNTs were placed separately in a
simulation box which has the same initial parameters with the single (10,10) nanotube
simulation which was performed in the first group. As a result of these simulations, no
effect of carbon nanotube number to the density in the nanotubes was observed.
 46

As a third group, (10,10) SWNT was used to observe the behavior of supercritical
CO2. Two simulations were performed in different box sizes while adding enough CO2
molecules to make the density of the system around 0.469 g/cm3 which is the critical
density of CO2. In the first simulation since box size was small compared the length of
nanotube, after a point, nanotube inside the box was appeared as if there were two
nanotubes and they caused each other to bend. The density inside nanotube was not 100
times higher than the bulk density as in the first group. In this case it was just twice. As a
second simulation, to decrease the effect of box size and tube length ratio, box size was
increased from 30x30x100 to 60x60x100 while keeping the density of the system as
critical density of CO2. However, the result did not change too much. Nanotube turned in
the box and separated into two parts due to the periodic boundary conditions again. And
the density inside nanotube was not different than the first simulation performed with
smaller box. However, the time required to reach the steady state is much smaller for
(10,10) SWNT system in supercritical CO2 environment rather than CO2.

5.2. RECOMMENDATIONS

Since the prepared simulations contain a lot of molecules, they needed lots of time to
reach the steady-state. To decrease the time effect, more powerful computers should be
used. Also, creating and running supercritical CO2 systems were impossible in big boxes
used in first group. Because it requires adding a lot of molecules compared to CO2 systems
and this limited us make a real comparison between CO2 confined in (10,10) SWNT with
supercritical CO2 confined in (10,10). Therefore box size was decreased and undesired
nanotube behavior was observed.

To be able to observe the effect of nanotube amount on fluid behavior, smaller

simulation box should be used or, nanotubes should be placed into the box as nanoropes.

As a future work, due to importance of water in each part of life, SWNT simulations
should be performed with water and also with other important fluids. Since, CO 2 forms a
hallow cylinder inside the nanotube, MWNTs should be studied for more effective CO2
removal.
 47

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