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ROLE OF FUNCTIONAL GROUP ON

ADSORPTION OF NATURAL GAS ON


GRAPHENE

Submitted by PARTHA PRATIM NIRMALIA(B090542CH)


PIJUSH KANTI BISWAS (B090837CH)
DEEPAK KUMAR (B090727CH)
SUMIT KUMAR (B090771CH)
AKASH SINGH (B090643CH)

Department of Chemical Engineering


National Institute of Technology
Calicut 673601 (India)

Abstract
Air quality is actually a major public health concern, especially in urban areas. The use of
clean fuels for vehicular applications is thus strongly encouraged. Natural gas, which primarily
consists of methane, is a valuable alternative fuel with major advantages as compared with gasoline,
namely: huge world reserves, low cost, clean burning characteristics (low emission levels and low
greenhouse impact) and greatest energy per unit mass of all the other hydrocarbons. However, since
supercritical in STP conditions, methane always has a very low density. Storing the greatest
amounts of methane in a given limited volume is thus a real challenge for its application to both gas
transportation and gas powered vehicles. Among the various storage methods used, adsorption using
appropriate materials is a technologically important method. Adsorbed natural gas (ANG) has the
potential to become the most cost-effective method compared to other methods such as liquefied
natural gas (LNG) and compressed natural gas (CNG).
In the recent years there has been a strong interest in developing materials for storage of
natural gas (methane). A while ago, the Atlanta Gas Light Adsorbent Research Group suggested the
target of 150 volumes of gas (measured in STP conditions) per volume of storage vessel (V/V)
delivered at 35 bars and 25 C for a viable application of natural gas vehicle. So far, much effort has
been made to produce materials that could adsorb and deliver such high amounts of gas. Adsorption
capacity of a material depends on its pore size and structure, and its surface chemistry. In the
present study, first we will start with the interaction potential for methane on benzene using the
classical potentials (Lennard-Jones Potential) is compared by varying the methane models (used
both the single site as well as five site methane model) and also changing the relative orientation of
5 site methane model over the centre of benzene ring starting with a initial orientation, to get the
most stable configuration for methanebenzene system. Also presents the potential energy curves
for different methane-benzene relative orientations. This study is done to start a study on the effect
of functional groups like of -OH, -NH2 and -COOH groups functionalized on graphene
nanoribbons, which is considered as one of the good adsorbent for methane. As the structural
aspects of graphene nanoribbons is somewhat resembles to that of benzene ring, so the interaction
of benzene-methane system has been studied first and we will compare the result with that of
benzene with functional group.

Contents
Abstract
1 Introduction
1.1 Importance of methane storage ...............................................................................
1.2 Alternative fuels available currently
1.3 Adsorbent materials..
1.4 Interaction potentials.
1.5 Rotation Matrices......................................................................................................

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4
4
6
7
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2 Method and Result


2.1 Introduction...............................................................................................................
2.2 Models of Methane....................................................................................................
2.3 Model of Benzene .
2.4 Interactions................................................................................................................
2.5 Results and conclusions.............................................................................................

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Appendix A
Appendix B
References

1. INTRODUCTION
1.1 Importance of methane storage
Despite technical advances to reduce air pollution emissions, motor vehicles still account for 30 to
70% emissions of all urban air pollutants. The Clean Air Act Amendments of 1990 require 100
cities in the United States to reduce the amount of their smog within 5 to 15 years. Hence, auto
emissions, the major cause of smog, must be reduced 30 to 60% by 1998. Some states like
California have set stringent laws to clean up severe air pollution. Beginning in 1997, 25% of all
cars sold in California must qualify as low emissions vehicles (LEVs). By 2005, 75% of the cars
sold in California must be LEVs. This type of situation has spurred interest in research and
development of alternative fuels.

1.2 Alternative fuels available currently


Electricity: Although electric vehicles (EV) do not produce tailpipe emissions, pollution is
produced at power plants that generate electricity to charge the vehicles batteries. If 50% of
the electricity is produced from coal, 20% from natural gas, and the remaining 30% from
nuclear or hydro power, then EVs will produce 99% less hydrocarbons, 99% less CO and
60% less NOx, compared with conventional gasoline fuelled vehicles. However, SOx and
particulate emissions could increase by a factor of five. Other pollutants can also result from
the use of batteries in vehicles. Water quality and solid waste disposal could be additional
environmental problems. EV can be used to reduce local air pollution in specific markets
such as vehicles for public services or urban use where speed and range are not limitations.
EVs are also recommended for those regions where fossil fuels are not the primary fuel used
to produce electricity.
Table 1: Equivalent ozone-producing potential for select vehicular fuels.
Fuels
Gasoline
M85 (85% methanol in gasoline)
M 100 ( 100% methanol)
CNG
LPG (Liquefied petroleum gas)

g of O3/mile
3.8
4.7
1.8
0.2
0.7

Methanol, liquefied petroleum gas and hydrogen: Vehicles operating with M85
(85%methanol/15% gasoline) or MlOO (pure methanol) have similar CO and NOx
emissions to conventional gasoline fuelled vehicles. The largest emission benefit from
methanol (MI 00) fuelled vehicles is their reduced ozone-producing potential (Table 1).
Emissions from liquefied petroleum gas (LPG) fuelled vehicles are comparable to gasoline
fuelled vehicles except for ozone formation. Hydrogen fuelled vehicles theoretically
produce no pollutants except NOx, which can be further reduced by lowering combustion

temperature. However, it is important to consider that hydrogen is made by coal gasification


or water electrolysis, and these processes generate air pollutants directly or indirectly.
Natural gas: Natural gas (NG), which primarily consists of methane, is a valuable
alternative fuel with major advantages as compared with gasoline, namely: huge world
reserves, low cost, clean burning characteristics (low emission levels and low greenhouse
impact) and greatest energy per unit mass of all the other hydrocarbons. A natural gas
vehicle (NGV) uses a conventional spark ignition engine with only minor modifications.
Natural gas burns more completely and produces less air pollutants than gasoline. There are
about 40,000 NGVs in the US and about one million worldwide. Emission data (Table 2)
how that NGVs, compared with conventional vehicles, have significantly lower CO
emissions due to better mixing of the gaseous fuel, lean fuel to air ratio and lack of fuel
enrichment to start. Carcinogenic pollutant (e.g., benzene and 1, 3-butadiene) emissions are
effectively eliminated. Because the hydrocarbon constituent in NGV exhaust is dominantly
methane, which has insignificant photochemical reactivity, emissions from NGV are
expected to contribute the least to ozone formation (Table 1).
Table 2. Reduction of emissions from NGV when compared to gasoline fuelled vehicle
Pollutants
CO
NOx
HCs (non-methane)
Benzene
1,3-butadiene

% Reduction
76
75
88
99
100

However, under ambient conditions methane is a supercritical gas (T c =190.3K; Pc = 45.96


bar) unlike gasoline which is a high density liquid. This implies that methane always has a very low
density and relatively large volumes of methane are required to generate energy equivalent to
gasoline, thereby increasing the cost in terms storage. Storing the greatest amounts of methane in a
given limited volume is thus a real challenge for its application to both gas transportation and gas powered vehicles. Large amounts of NG are stored naturally underground in facilities like depleted
oil reservoirs and aquifers. The gas from these underground sites is pumped up to the ground for
use. On the ground, different methods are used for storage.
There are three technologies for on-board natural gas storage:
1. liquefied natural gas (LNG):
In the LNG process, the gas is stored and transported by liquefying at atmospheric pressure
and 112 K. This requires cryogenic technology to maintain such low temperature and hence is
expensive for domestic purposes. This storage process is useful when transportation of the gas is not
possible through pipelines.
2. compressed natural gas (CNG):
In the CNG process, the gas is stored in gaseous form but under very high pressure (200-250
bar) at room temperature. Since the process involves very high pressure, it requires multistage
compression, sturdy materials for containers and associated pumping costs. Its energy density is
21% of that of gasoline, lower than that of LNG. Nevertheless this storage system has been
commercialized for transportation in certain parts of the world where it has been found to be 25%
cheaper than gasoline powered transportation.

3. adsorbed natural gas (ANG):


In the ANG process, the gas is stored in an adsorbed state in a micro porous adsorbent
material. ANG has the lowest volumetric energy density among the storage methods. However it
has the potential to be one of the least expensive depending on the type of adsorbent material.
Hence there is a need to discover and synthesize a material which can store large amount of the gas
and hence increase its volumetric energy density. In order for ANG to achieve an energy density
equal to that of the commercialized CNG system, the US Department of Energy has set the target
for storage density as 180 V/V, which means the ratio of the volume of the stored gas at 35 bar and
298K to the volume of the same amount at standard conditions (1 bar and 298 K) is 180 to 1. The
search for a novel material which can achieve this target is an active area of research and hence
forms the motivation for the present study.

1.3 Adsorbent materials


Adsorption is the adhesion of atoms, ions, or molecules from a gas, liquid, or dissolved solid to
a surface. This process creates a film of the adsorbate on the surface of the adsorbent. It is a surface
phenomenon and is a consequence of surface energy. In the process of adsorption, the gas from the
bulk gets adsorbed onto the surface of the adsorbent under the influence of attractive surface forces.
This can happen in two ways: by chemisorption, which involves breaking/formation of chemical
bonds and physisorption, where the chemical nature of the gas (adsorbate) does not change. The
success of the adsorption capture/separation process depends a lot on the nature of the adsorbent
material. Adsorbents are highly micro porous materials with very high surface area. The size and
shape of the pores along with the type of material, affects its performance. Hence choosing an
adsorbent for a particular application will depend mainly on these factors.
A variety of materials have been identified as potential adsorbents for methane (see Tables 3)
and are classified by a variety of criteria like chemical composition, pore size etc. Zeolites, carbons
and metal organic frameworks have pore dimensions of the order of molecular size.
1. Zeolites are naturally occurring aluminosilicates. Their topology consists of a network of
interconnecting channels and/or cages. One of the main disadvantages of zeolites is that
their surface area cannot be increased beyond a certain limit (1000 m 2/g). In addition to this,
they are hydrophilic and hence their performance may be reduced in the presence of water.
However, zeolites with high silicon content are hydrophobic and hence may be helpful
where water is hindering the adsorption process.
2. Metal organic frameworks are novel materials in this field of gas storage, characterized by
very large pores, composed of both inorganic and organic building blocks. They have cagelike structure made up of metal-atom-cores linked with organic linker molecules. The linker
molecules are organic which may be functionalized with various functional groups. As the
values ( in table 4) indicates, MOFs have the ability to adsorb huge quantities of CH4 .The
ease with which their chemical composition can be varied by modifying their synthesis
techniques makes them very attractive for research. Modifications are mainly done by
attaching functional groups on the linker molecules and studying their effect on gas uptake.
Presently, these materials are still being researched on laboratory scale.
3. Activated carbons are another class of potential adsorbents in this area, as they have very
high surface area. Unlike zeolites and MOFs, they have distribution in the pore size and

shapes. The activated carbons have an advantage over zeolites in terms of hydrophobicity
and also can attain very high surface area. Compared to MOFs, the activated carbons are
less expensive to produce. The strength of these materials lies in the fact that they can be
prepared from less expensive precursor materials like coconut shell, corn grain, fruit stones,
coals etc.

Table 3: Adsorbent materials for methane adsorption at 35 bar.


Adsorbent

T (K)

Amount adsorbed
( Mmolg-1 )

NaX

298

66

NaY

298

56

CaX

298

82

298

44

PX-21, Amoco (Maxsorb)

298

177

Kansai Maxsorb

298

164

PCN-14

298

230

MIL-53

298

155

Zeolite

Silicalite
Activated Carbon

Metal-organic frameworks

The adsorbent materials typically do not exhibit uniform adsorption throughout the material.
Certain sites on the material preferentially adsorb gases more than others and are referred to as
adsorption or binding sites. Location of the adsorption sites on the material depends on its structure
and chemistry. These sites may be functional groups, and defects on the material, etc. Hence careful
consideration needs to be give to the chemistry and structure while choosing an adsorbent for
certain application. Metal atoms, nucleophiles, acids, bases, hydrogen bond donors and acceptors
are collectively termed as functional groups. Apart from adsorption, functional groups play
important roles in other applications like catalysis, drug delivery and nanotechnology. Hence
fictionalization of materials in order to obtain certain specific characteristics is an active area of
research in the field of synthetic chemistry.

1.4 Interaction potentials


The interaction between two molecules separated by some distance r is modelled as a sum of
Lennard-Jones and Coulombic potential energies.

Lennard-Jones Potential

The Lennard-Jones potential (also referred to as the L-J potential, 6-12 potential, or 12-6 potential)
is a mathematically simple model that approximates the interaction between a pair of neutral atoms
or molecules. A form of the potential was first proposed in 1924 by Sir John Edward Lennard-jones.

Where,
V is the intermolecular potential between the two atoms or molecules,
is the depth of the potential well and a measure of how strongly the two particles attract each
other,
is the distance at which the intermolecular potential between the two particles is zero. It gives a
measurement of how close two nonbonding particles can get and is thus referred to as the van der
waals radius, and
r is the distance of separation between both particles (measured from the centre of one particle to
the centre of the other particle), generally referred as Lennard-Jones separation distance.
and are called as LJ parameters and they depends on the nature of molecules present for interaction.

Figure 1: Lennard-Jones potential curve with parameters.


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The term r

, dominating at short distance, models the repulsion between atoms when they are

brought very close to each other. Its physical origin is related to the Pauli principle: when the
electronic cloud surrounding the atoms starts to overlap, the energy of the system increases
abruptly. The exponent 12 was chosen exclusively on a practical basis. In fact, on physical grounds
an exponential behaviour would be more appropriate.
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The term r , dominating at large distance, constitute the attractive part. This is the term which
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gives cohesion to the system. A r attraction is originated by Van der Waals dispersion forces,
originated by dipole-dipole interactions in turn due to fluctuating dipoles.
Bonding Potential
As mentioned earlier, the Lennard-Jones Potential is a function of the distance between the
centres of two particles. When two nonbonding particles are an infinite distance apart, the
possibility of them coming together and interacting is minimal. For the sake of simplicity then, we
can say that their bonding potential energy is zero. However, as the distance of separation decreases,
the probability of interaction increases. The particles come closer together until they reach a region
of separation where the two particles become bound and their bonding potential energy decreases
from zero to become a negative quantity. While the particles are bound, the distance between their
centres will continue to decrease until the particles reach an equilibrium, which is specified by the
separation distance at which the minimum potential energy is reached. Now, if we keep pushing the
two bound particles together passed their equilibrium distance, repulsion begins to occur, as
particles are so close to each other that their electrons are forced to occupy each others orbital.
Therefore, repulsion occurs as each particle attempts to retain the space in their respective orbital.
Despite the repulsive force between both particles, their bonding potential energy rises rapidly as
the distance of separation between them decreases below the equilibrium distance.

Figure 2: The interaction phenomenon can be view as two spherical balls separated by distance r.
Stability and Force of Interactions
Very much like the bonding potential energy, the stability of an arrangement of atoms is also
a function of the Lennard-Jones separation distance. As the separation distance decreases below
equilibrium the potential energy becomes increasingly positive (force is repulsive). Such a large
potential energy is energetically unfavourable as it indicates an overlapping of atomic orbital.
However, at long separation distances, the potential energy is negative and approaches zero as the
separation distance increases to infinity (force is attractive). This indicates that at such long-range
distances, the pair of atoms or molecules experiences a small stabilizing force. Lastly, as the
separation between the two particles reaches a distance slightly greater than , the potential energy
reaches a minimum value (force is zero). At this point, the pair of particles is most stable and will
remain in that orientation until an external force is exerted upon them.

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Figure 3: Lennard-Jones potential curve with forces.

Coulombic Potential
The Lennard--Jones potential is one important part of the interaction between two molecules. The
second part of the interaction is due to forces between electrical charges and is called by coulombic
potential. Interactions between two molecules due to their permanent dipole moments are described
approximately by treating the charged portions of the molecule as point charges. The Coulomb
potential is an effective pair potential that describes the interaction between two point charges. It
acts along the line connecting the two charges. It is given by the equation:

where
r is the distance between two ions,
q1 and q2 are the electric charge in coulombs carried by charge 1 and 2 respectively, and
0 is the electrical permittivity of space.
Two oppositely charged particles will give an attractive potential, whereas if both particles are of
the same sign (i.e., both are positive or both are negative) the potential is repulsive. The resulting
potential is shown in Figure 4.

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Figure 4: The Coulomb potential. The bottom curve represents the interaction between two
particles of opposite charge; the top curve represents the interaction of particles of equal charge.

1.5 Rotation Matrices


In linear algebra, a rotation matrix is a matrix that is used to perform a rotation in Euclidean space.
For example the matrix

rotates points in the xy-Cartesian plane counterclockwise through an angle about the origin of
the Cartesian coordinate system. To perform the rotation using a rotation matrix R, the position of
each point must be represented by a column vector v, containing the coordinates of the point. A
rotated vector is obtained by using the matrix multiplication Rv. Since matrix multiplication has no
effect on the zero vector (i.e., on the coordinates of the origin), rotation matrices can only be used to
describe rotations about the origin of the coordinate system.
The following three basic rotation matrices rotate vectors about the x, y, or z axis, in three
dimensions:

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These rotation matrices has been used in this study for changing the relative orientation of 5-site
methane molecule over benzene centre, by rotating the methane molecule along x, y and z-axis
starting from the initial orientation.

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2. METHOD AND RESULT


2.1 Introduction
In this chapter interaction potential curve are plotted by writing small programs (using C++ programing ) for
both one site and five site model of methane by varying distance between the centre of methane and the
centre of benzene ring. Also the five site model has been given various orientations keeping the C-atom of
methane fix above the benzene ring centre to find the orientation with minimum possible well. We need to
find the minimum possible well in case of methane benzene system in order to check its most stable
orientation.

2.2 Models of Methane

Figure 5: Methane models used in the present calculations. The bond angles and bond lengths
shown for the five-site methane model are similar for all the bonds and angles.
There are two widely used classical models for methane, namely the one-site and Kollman five-site
models. The parameters for the one-site model were developed using the vapour-liquid equilibrium data
whereas those for the Kollman five-site model was based on free energy calculations to predict solvation of a
methane molecule in bulk water. Both the models successfully reproduce the fluid-phase behaviour of

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methane. The charges and the LJ parameters for the two models are shown in the Table 3. In the rigid
Kollman five-site model intermolecular site-site interactions are treated using the 12-6 Lennard-Jones
interaction potential and Coulombic interactions are used for interactions between charges. Both the five-site
and one-site models are depicted in the Figure 5.

Table 4 : Lennard-Jones parameters and Coulombic charges for one-site and five-site
methane models.

(A)

One-site
model
3.73

(K)

148

q (e)

0.0

Five-site model
C
H
C
H
C
H

3.4
2.65
55.055
7.901
-0.66
0.165

2.3 Model of Benzene

Figure 6: Benzene models used in the present calculations. The bond angles and bond lengths
shown for the five-site methane model are similar for all the bonds and angles.

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Benzene is an organic chemical compound with the molecular formula C6H6. Its molecule is
composed of 6 carbon atoms joined in a ring, with 1 hydrogen atom attached to each carbon atom.
Because its molecules contain only carbon and hydrogen atoms, benzene is classed as a
hydrocarbon.

Table 5: Lennard-Jones parameters and Coulombic charges for Benzene model.


(A)
(K)
q (e)

C
H
C
H
C
H

Benzene
3.75
0.0
55.3541
0.0
0.0
0.0

2.4 Interactions
The interactions are between methane molecules and benzene. The interaction between sites 1 and 2
on the molecules, which are modeled as a sum of Lennard-Jones and Coulombic potential energies,
are given as

....................... 2.1
where
1,2 is the effective Lennard-Jones diameter, evaluated using equation 2.2
1,2 is the effective well depth, evaluated using equation 2.3
r1,2 is the distance between the interacting sites,
q1 , q2 are Coulombic charges of the interacting sites, and
0 is a constant called the permittivity of free space.
The interaction between two molecules separated by some distance r are modelled as a sum
of Lennard-Jones and Coulombic potential energies but for methane benzene system the net
interaction is Lennard-Jones potential energy only. The reason is that the C and H atom of benzene
have no net charges so the coulombic part for both one-site and five-site model of methane with
benzene will be zero.
The effective Lennard-Jones diameter and well-depth for interaction between two different species
is given by the Lorentz-Berthelot mixing rule

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......................................................................................................2.2

...........................................................................................................2.3
where
i is the Lennard-Jones diameter for the ith species,
i is the well depth for the ith species.
1. Interaction of one-site methane with benzene:
The potential curve for one-site methane and benzene is obtained by placing the methane molecule
at different positions along the axis passing through the centre of the benzene ring. In this system
only Lennard-Jones interaction is there as told earlier the coulombic part is zero for methanebenzene system. Program 1 (in appendix B) is written ( in C language) to calculate the potential
energy at around 100 different positions along the axis passing through the centre of the benzene
ring using the equation where the Lennard-Jones parameters for one-site methane is given in table 4
and for benzene in table 5. The curve obtained through this program is shown in figure 7. The
minimum potential energy well obtained in this case is around -4.6 kJ/mol at a seperation of 3.98

angstrom which matches with the Vinay's thesis (IISc Bangalore).


Figure 7 : Potential energy curve for 1-site methane model over benzene.

2. Interaction of five-site methane with benzene:


The potential energy curve for five-site methane and benzene is obtained by placing the methane
molecule at different positions along the axis passing through the centre of the benzene ring. But in
case of five-site methane the calculation of minimum energy well is much more complicated as
compared to the previous system. In this system also only Lennard-Jones interaction is there, as the

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coulombic part is zero for methane-benzene system, but this system gives different potential energy
well for different orientation with respect to benzene ring, not like that in case of one-site methane
which gives only a single minimum potential well. So in order to find the minimum potential well
for five-site methane-benzene system, the methane molecule is placed over the centre of benzene
ring and given 1400 random rotations about its centre of mass and then for every rotation ( starting
from the initial orientation ) the potential energy at around 100 different positions along the axis
passing through the centre of the benzene ring is calculated using the equation where the LennardJones parameters for five-site methane is given in table 4 and for benzene in table 5.
Many small programs are written to plot the potential energy curve, to find the minimum
energy well among all orientation possible and corresponding separation. I started calculating the
interaction potential from the initial orientation of methane benzene system given to me shown in
figure 8. The coordinates of initial five-site methane and benzene is given in coordinate-2 and
coordinate-1 (in appendix A) respectively.

Figure 8: Initial orientation of methane benzene system.


I proceed through following steps to find the minimum potential well for five-site methanebenzene system.
1. Calculation of the potential energy at around 100 different positions along the axis passing
through the centre of the benzene ring for the initial orientation of methane molecule ( CH down)
over benzene as shown in figure (using program 2),using the equation where the Lennard-Jones
parameters for five-site methane is given in table 4 and for benzene in table 5. The curve obtained
is shown in figure 9. The minimum potential energy well obtained in this case is around -4.385
kJ/mol at a separation of 4.15 angstroms.

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Figure 9: Potential energy curve for 5-site methane model (CH down) over benzene.
2. Rotating the five-site methane molecule about its centre of mass along x and y-axis and finding
the orientation with minimum energy for methane-benzene system. The methane molecule is placed
over the centre of benzene ring and given 1400 random rotations about its centre of mass using
rotation matrices (already included it in introduction) along each of x and y-axis and then for every
rotation (starting from the initial orientation) the potential energy at around 100 different positions
along the axis passing through the centre of the benzene ring is calculated by writing program 3 and
program 4 (appendix B). From the program 3 and 4 I got that the minimum energy orientation of
methane-benzene system after giving methane molecule a 1400 rotation about its centre of mass
along each of x and y-axis are same and its shown in figure 10, which is a 180 degree position
( CH-up) as compared to the initial position of methane. The coordinates of five-methane
corresponds to minimum energy orientation after rotation along x and y is given in coordinates 3
and 4 (appendix A) respectively.

Figure 10: Most stable configuration after rotating the five-site methane molecule about its centre
of mass along x and y-axis
3. Calculating the value of minimum energy well by plotting potential energy curve for the
orientation of methane with CH-up shown in figure. This is done by writing program 5 (appendix
B) using the coordinates of five-site methane molecule with CH-up and benzene from the

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coordinate-3 and coordinate-1(appendix A). Like for initial orientation of methane, for this
orientation also the potential energy is calculated at around 100 different positions along the axis
passing through the centre of the benzene ring using the equation. The curve obtained is shown in
figure 11. The minimum potential energy well obtained in this case comes out to be around -6.0643
kJ/mol at a separation of 3.74 angstroms. These values matches with Vinay's thesis and CCSD (T)
(Tsuzuki et al., 2000; Ashley et al., 2006) but the orientation doesn't.

Figure 11: Potential energy curve for 5-site methane model (CH up) over benzene.
4. Rotating the five-site methane molecule (with CH-up) shown in figure 10, about its centre of
mass along z-axis, finding the orientation with minimum energy and calculating the difference
between minimum and maximum energy well in interaction of 5-site methane-benzene system
using program 6 (appendix B). The difference in energy well is merely 0.0031 kJ/mol shown in
figure 12, where energy is plotted against the degree of rotation along z-axis. The minimum energy
orientation is shown in figure 15 and corresponding energy well is -6.0663 kJ/mol. This the
minimum potential energy well in five-site methane and benzene interaction.

Figure 12: Variation of energy with rotation along z-axis

2.5 RESULTS AND CONCLUSIONS


For 5-site methane model with CH-up orientation is more stable than the one with CH-down
over benzene as shown in figure 13, where potential energy curves for both orientation has been
compared.

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Figure 13: Comparison of potential curves for 5-site methane over benzene with its CH-up and
CH-down orientation.

In all cases we observed that the single site models for methane predict a lower binding
energy when compared with the five-site model (with CH up) as shown in figure14.

Figure 14: Comparison of potential curves for 5-site methane with its CH-up and
CH-down orientation and 1-site methane over benzene.
The most stable orientation of methane-benzene system is shown in figure 10, with
minimum energy well of -6.0663 kJ/mol and corresponding interatomic distance of 3.74
angstroms.

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Appendix A
coordinates 1-coordinates of benzene
C1
C2
C3
H
H
C4
C5
H
H
C6
H
H

1.375176933
0.665644160
0.709532773
1.183516950
1.261551005
-0.709532773
-0.665644160
-1.261551005
-1.183516950
-1.375176933
-2.445067955
2.445067955

-0.025339102
-1.203607710
1.178268607
-2.140017455
2.094964472
-1.178268607
1.203607710
-2.094964472
2.140017455
0.025339102
0.045052983
-0.045052983

-0.817565265
-0.817565247
-0.817565247
-0.817565256
-0.817565256
-0.817565265
-0.817565265
-0.817565256
-0.817565256
-0.817565247
-0.817565256
-0.817565256

coordinates 2-Initial coordinates of 5-site methane


C0
H1
H2
H3
H4

0.000000000
-0.993995285
0.718721927
0.275273359
0.000000000

0.000000000
-0.256025150
-0.732812593
0.988837743
0.000000000

3.981339030
4.343180607
4.343180607
4.343180607
2.895814297

coordinates 3-coordinates of 5-site methane with minimum energy well after rotating intial methane
coordinates along x-axis about its c-atom

c0
H1

0.000000
-0.999953

0.000000
0.256030

3.98134
3.61950

22

H2
H3
H4

0.718722
0.275273
0.000000

0.732818
-0.988832
0.000000

3.61951
3.61948
5.06686

coordinates 4-coordinates of 5-site methane with minimum energy well after rotating intial methane
coordinates along y-axis about its c-atom

c0
H1
H2
H3
H4

0.000000
0.999953
-0.718722
-0.275273
0.000000

0.000000
-0.256030
-0.732818
0.988832
0.000000

3.98134
3.61950
3.61951
3.61948
5.06686

coordinates 5-coordinates of 5-site methane with minimum energy well after rotating the CH up
methane molecule along z-axis about its c-atom
c0
H1
H2
H3
H4

0.0000000
-0.899616
0.8838980
0.0099636
0.0000000

0.000000
0.506108
0.521824
-1.02639
0.000000

3.98134
3.61950
3.61950
3.61950
5.06686

Appendix B
Programs
program 1 : CALCULATING THE MINIMUM ENERGY WELL IN INTERACTION OF 1SITE METHANE WITH BENZENE
#include<iostream>
#include<iomanip>
#include<cstdio>
#include<cmath>
#include<fstream>
#include<stdlib.h>
#include<time.h>
#include<limits>
using namespace std;
using std::numeric_limits;
int main()
{
float a=92.3222,b=3.74,min,max,c,inc;
float r[100],u[100],v[100];
float minele,mindis;
cout<<"Enter the min and max distance of methane centre from benzene centre in amgstrom : ";
cin>>min>>max;
c=(1.38*6.022)/1000;

//conversion of unit of energy from K to kJ/mol

23

inc=((max-min)/100);
v[0]=min;
for(int i=0;i<=99;i++)
//finding energy corresponds to different seperation distance
{
r[i]=pow((pow(1.3754,2)+pow(min,2)),0.5);
u[i]=c*6*4*a*(pow(b/r[i],12)-pow(b/r[i],6));
cout<<"\n"<<"Distance (in amgstron) : "<<min;
cout<<"\t"<<"Energy (in kJ/mol):"<<u[i];
v[i+1]=min+inc;
min=v[i+1];
}
minele=u[0];
mindis=v[0];

//finding the minimum energy well and corresponding distance

for(int j=0;j<=90;j++)
{
if(u[j]<minele)
{
minele=u[j];
mindis=v[j];
}
}
cout<<"\n"<<"\n"<<"\n"<<"Minimum energy well = "<<minele<<" kJ/mol ";
cout<<"\n"<<"at a distance of = "<<mindis<<" amgstrom ";
ofstream fp;
fp.open("one.txt");
for(int j=0;j<=99;j++)
{
fp<<v[j]<<"\t"<<u[j]<<"\n";
}
fp.close();

// storing the values of distance and energy in a file

return(0);
}

24

program 2 : CALCULATING THE MINIMUM ENERGY WELL IN INTERACTION OF 5SITE METHANE (0 degree i.e, CH down) WITH BENZENE
#include<iostream>
#include<iomanip>
#include<cstdio>
#include<cmath>
#include<fstream>
#include<stdlib.h>
#include<time.h>
#include<limits>
using namespace std;
using std::numeric_limits;
int main()
{
float a=59.06865175,b=3.575,c=22.37689,d=3.2,min,max,v,x,p,inc;
float r[100],r0[100],r11[100],r12[100],r13[100],r14[100],r15[100],r16[100],r4[100],u0[100],
u11[100],u12[100],u13[100],u14[100],u15[100],u16[100],u1[100],u4[100],u[100];
float minele,mindis;
cout<<"Enter the min and max distance coordinate of benzene from methane ( if carbon of methane
at coordinate z=3.98 and is above benzene): ";
cin>>min>>max;
p=(1.38*6.022)/1000;
inc=((min-max)/100);

//conversion of unit of energy from K to kJ/mol

for(int i=0;i<=99;i++)

//finding energy corresponds to different seperation distance

is

25

{
//interaction of C0 of methane with that of benzene
r0[i]=pow(1.891753667+pow(3.98133903-min,2),0.5);
u0[i]=6*4*a*(pow(b/r0[i],12)-pow(b/r0[i],6));
//interaction of H4 of methane with C of benzene
r4[i]=pow(1.891753667+pow(2.895814297-min,2),0.5);
u4[i]=6*4*c*(pow(d/r4[i],12)-pow(d/r4[i],6));
//interaction of H1 of methane with C of benzene
x=pow(4.343180607-min,2);
r11[i]=pow(5.694457539+x,0.5);
r12[i]=pow(3.67212611+x,0.5);
r13[i]=pow(4.979539677+x,0.5);
r14[i]=pow(0.934876815+x,0.5);
r15[i]=pow(2.242290386+x,0.5);
r16[i]=pow(0.2314411546+x,0.5);
u11[i]=4*c*(pow(d/r11[i],12)-pow(d/r11[i],6));
u12[i]=4*c*(pow(d/r12[i],12)-pow(d/r12[i],6));
u13[i]=4*c*(pow(d/r13[i],12)-pow(d/r13[i],6));
u14[i]=4*c*(pow(d/r14[i],12)-pow(d/r14[i],6));
u15[i]=4*c*(pow(d/r15[i],12)-pow(d/r15[i],6));
u16[i]=4*c*(pow(d/r16[i],12)-pow(d/r16[i],6));
u1[i]=3*(u11[i]+u12[i]+u13[i]+u14[i]+u15[i]+u16[i]);
//total potential enegy
u[i]=p*(u0[i]+u1[i]+u4[i]);
r[i]=3.98133903-min;

cout<<"\n"<<"Distance (in amgstron) : "<<r[i];


cout<<"\t"<<"Energy (in kJ/mol):"<<u[i];
v=min-inc;
min=v;

}
minele=u[0];
mindis=r[0];

//finding the minimum energy well and corresponding distance

for(int j=0;j<=99;j++)
{
if(u[j]<minele)
{
minele=u[j];
mindis=r[j];
}

26

}
cout<<"\n"<<"\n"<<"\n"<<"Minimum energy well for 0 deg(i.e, CH down) positon of methane =
"<<minele<<" kJ/mol";
cout<<"\n"<<"at a distance of = "<<mindis<<" amgstrom";

ofstream fp;
fp.open("five.txt");
for(int j=0;j<=99;j++)
{
fp<<r[j]<<"\t"<<u[j]<<"\n";
}
fp.close();

//storing the values of distance and energy in a file

return(0);
}

program 3 : ROTATING THE 5-SITE METHANE MOLECULE ALONG X-AXIS ABOUT


ITS C-ATOM AND CALCULATING THE MINIMUM ENERGY WELL IN
INTERACTION OF 5-SITE METHANE WITH BENZENE
#include<iostream>
#include<iomanip>
#include<cstdio>
#include<cmath>
#include<fstream>
#include<stdlib.h>
#include<time.h>
#include<limits>
using namespace std;
using std::numeric_limits;
int main()
{
float a=59.06865175,b=3.575,c=22.37689,d=3.2,min,mini,max,v,convo,maxangle=(2*3.141592654),angle,
minangle=0,inc,incd;
float xh1,yh1,zh1,newxh1,newyh1,newzh1,xh2,yh2,zh2,newxh2,newyh2,newzh2,xh3,yh3,zh3,newxh3,
newyh3,newzh3,xh4,yh4,zh4,newxh4,newyh4,newzh4;
float r[100],r0[100],u0[100],u1[100],u2[100],u3[100],u4[100],u[100];

27

float r11[100],r12[100],r13[100],r14[100],r15[100],r16[100],u11[100],u12[100],u13[100],u14[100],
u15[100],u16[100],r21[100],r22[100],r23[100],r24[100],r25[100],r26[100],u21[100],u22[100],u23[100],
u24[100],u25[100],u26[100],r31[100],r32[100],r33[100],r34[100],r35[100],r36[100],u31[100],u32[100],
u33[100],u34[100],u35[100],u36[100],r41[100],r42[100],r43[100],r44[100],r45[100],r46[100],u41[100],
u42[100],u43[100],u44[100],u45[100],u46[100];
float h1[3][1],h2[3][1],h3[3][1],h4[3][1],x[3][3],newx1[3][1],newx2[3][1],newx3[3][1],newx4[3][1];
float minelement[1400],mindistance[1400],minele,mindis,mminelement,mmindistance,orientation[1400],
oorientation;
cout<<"Enter the min and max distance coordinate of benzene from methane ( if carbon of methane is at
coordinate z=3.98 and is above benzene): ";
cin>>mini>>max;
inc=(maxangle-minangle)/1440;
incd=(mini-max)/100;
convo=(1.38*6.022)/1000;

//conversion of unit of energy from K to kJ/mol

//rotation of methane along x-axis about its c-atom


for(int o=0;o<=1400;o++)
{
min=mini;
for(int i=0;i<=99;i++)
{
//interaction of C0 of methane with that of benzene
r0[i]=pow(1.891753667+pow(3.98133903-min,2),0.5);
u0[i]=6*4*a*(pow(b/r0[i],12)-pow(b/r0[i],6));
//coordinates of H4 with origin at centre of C-atom of methane
xh4=0;
yh4=0;
zh4=-1.085524733;
xh1=-0.99995285;
yh1=-0.25602515;
zh1=0.361841577;
xh2=0.718721927;
yh2=-0.732812593;
zh2=0.361841577;
xh3=0.275273359;
yh3=0.988837743;
zh3=0.361841577;

h4[0][0]=xh4; h4[1][0]=yh4; h4[2][0]=zh4;


h1[0][0]=xh1; h1[1][0]=yh1; h1[2][0]=zh1;
h2[0][0]=xh2; h2[1][0]=yh2; h2[2][0]=zh2;
h3[0][0]=xh3; h3[1][0]=yh3; h3[2][0]=zh3;

28

x[0][0]=1; x[1][0]=0; x[2][0]=0; x[0][1]=0; x[1][1]=cos(minangle); x[2][1]=-sin(minangle); x[0][2]=0;


x[1][2]=sin(minangle); x[2][2]=cos(minangle);
for(int j=0;j<3;j++)
{
for(int k=0;k<1;k++)
{
newx4[j][k]=0;
newx1[j][k]=0;
newx2[j][k]=0;
newx3[j][k]=0;
for(int l=0;l<3;l++)
{
newx4[j][k]=newx4[j][k]+(x[j][l]*h4[l][k]);
newx1[j][k]=newx1[j][k]+(x[j][l]*h1[l][k]);
newx2[j][k]=newx2[j][k]+(x[j][l]*h2[l][k]);
newx3[j][k]=newx3[j][k]+(x[j][l]*h3[l][k]);
}
}
}

newxh4=newx4[0][0];
newyh4=newx4[0][1];
newzh4=newx4[0][2]+3.981339030;
newxh1=newx1[0][0];
newyh1=newx1[0][1];
newzh1=newx1[0][2]+3.981339030;
newxh2=newx2[0][0];
newyh2=newx2[0][1];
newzh2=newx2[0][2]+3.981339030;
newxh3=newx3[0][0];
newyh3=newx3[0][1];
newzh3=newx3[0][2]+3.981339030;
//interaction of H4 of methane with that of benzene
r41[i]=pow(pow(newxh4-1.375176933,2)+pow(newyh4+0.025339102,2)+pow(newzh4-min,2),0.5);
r42[i]=pow(pow(newxh4-0.665644160,2)+pow(newyh4+1.203607710,2)+pow(newzh4-min,2),0.5);
r43[i]=pow(pow(newxh4-0.709532773,2)+pow(newyh4-1.178268607,2)+pow(newzh4-min,2),0.5);
r44[i]=pow(pow(newxh4+0.709532773,2)+pow(newyh4+1.178268607,2)+pow(newzh4-min,2),0.5);
r45[i]=pow(pow(newxh4+0.665644160,2)+pow(newyh4-1.203607710,2)+pow(newzh4-min,2),0.5);
r46[i]=pow(pow(newxh4+1.375176933,2)+pow(newyh4-0.025339102,2)+pow(newzh4-min,2),0.5);
u41[i]=4*c*(pow(d/r41[i],12)-pow(d/r41[i],6));
u42[i]=4*c*(pow(d/r42[i],12)-pow(d/r42[i],6));
u43[i]=4*c*(pow(d/r43[i],12)-pow(d/r43[i],6));
u44[i]=4*c*(pow(d/r44[i],12)-pow(d/r44[i],6));
u45[i]=4*c*(pow(d/r45[i],12)-pow(d/r45[i],6));
u46[i]=4*c*(pow(d/r46[i],12)-pow(d/r46[i],6));
u4[i]=u41[i]+u42[i]+u43[i]+u44[i]+u45[i]+u46[i];

29

//interaction of H1 of methane with that of benzene


r11[i]=pow(pow(newxh1-1.375176933,2)+pow(newyh1+0.025339102,2)+pow(newzh1-min,2),0.5);
r12[i]=pow(pow(newxh1-0.665644160,2)+pow(newyh1+1.203607710,2)+pow(newzh1-min,2),0.5);
r13[i]=pow(pow(newxh1-0.709532773,2)+pow(newyh1-1.178268607,2)+pow(newzh1-min,2),0.5);
r14[i]=pow(pow(newxh1+0.709532773,2)+pow(newyh1+1.178268607,2)+pow(newzh1-min,2),0.5);
r15[i]=pow(pow(newxh1+0.665644160,2)+pow(newyh1-1.203607710,2)+pow(newzh1-min,2),0.5);
r16[i]=pow(pow(newxh1+1.375176933,2)+pow(newyh1-0.025339102,2)+pow(newzh1-min,2),0.5);
u11[i]=4*c*(pow(d/r11[i],12)-pow(d/r11[i],6));
u12[i]=4*c*(pow(d/r12[i],12)-pow(d/r12[i],6));
u13[i]=4*c*(pow(d/r13[i],12)-pow(d/r13[i],6));
u14[i]=4*c*(pow(d/r14[i],12)-pow(d/r14[i],6));
u15[i]=4*c*(pow(d/r15[i],12)-pow(d/r15[i],6));
u16[i]=4*c*(pow(d/r16[i],12)-pow(d/r16[i],6));
u1[i]=u11[i]+u12[i]+u13[i]+u14[i]+u15[i]+u16[i];
//interaction of H2 of methane with that of benzene
r21[i]=pow(pow(newxh2-1.375176933,2)+pow(newyh2+0.025339102,2)+pow(newzh2-min,2),0.5);
r22[i]=pow(pow(newxh2-0.665644160,2)+pow(newyh2+1.203607710,2)+pow(newzh2-min,2),0.5);
r23[i]=pow(pow(newxh2-0.709532773,2)+pow(newyh2-1.178268607,2)+pow(newzh2-min,2),0.5);
r24[i]=pow(pow(newxh2+0.709532773,2)+pow(newyh2+1.178268607,2)+pow(newzh2-min,2),0.5);
r25[i]=pow(pow(newxh2+0.665644160,2)+pow(newyh2-1.203607710,2)+pow(newzh2-min,2),0.5);
r26[i]=pow(pow(newxh2+1.375176933,2)+pow(newyh2-0.025339102,2)+pow(newzh2-min,2),0.5);
u21[i]=4*c*(pow(d/r21[i],12)-pow(d/r21[i],6));
u22[i]=4*c*(pow(d/r22[i],12)-pow(d/r22[i],6));
u23[i]=4*c*(pow(d/r23[i],12)-pow(d/r23[i],6));
u24[i]=4*c*(pow(d/r24[i],12)-pow(d/r24[i],6));
u25[i]=4*c*(pow(d/r25[i],12)-pow(d/r25[i],6));
u26[i]=4*c*(pow(d/r26[i],12)-pow(d/r26[i],6));
u2[i]=u21[i]+u22[i]+u23[i]+u24[i]+u25[i]+u26[i];
//interaction of H3 of methane with that of benzene
r31[i]=pow(pow(newxh3-1.375176933,2)+pow(newyh3+0.025339102,2)+pow(newzh3-min,2),0.5);
r32[i]=pow(pow(newxh3-0.665644160,2)+pow(newyh3+1.203607710,2)+pow(newzh3-min,2),0.5);
r33[i]=pow(pow(newxh3-0.709532773,2)+pow(newyh3-1.178268607,2)+pow(newzh3-min,2),0.5);
r34[i]=pow(pow(newxh3+0.709532773,2)+pow(newyh3+1.178268607,2)+pow(newzh3-min,2),0.5);
r35[i]=pow(pow(newxh3+0.665644160,2)+pow(newyh3-1.203607710,2)+pow(newzh3-min,2),0.5);
r36[i]=pow(pow(newxh3+1.375176933,2)+pow(newyh3-0.025339102,2)+pow(newzh3-min,2),0.5);
u31[i]=4*c*(pow(d/r31[i],12)-pow(d/r31[i],6));
u32[i]=4*c*(pow(d/r32[i],12)-pow(d/r32[i],6));
u33[i]=4*c*(pow(d/r33[i],12)-pow(d/r33[i],6));
u34[i]=4*c*(pow(d/r34[i],12)-pow(d/r34[i],6));
u35[i]=4*c*(pow(d/r35[i],12)-pow(d/r35[i],6));
u36[i]=4*c*(pow(d/r36[i],12)-pow(d/r36[i],6));
u3[i]=u31[i]+u32[i]+u33[i]+u34[i]+u35[i]+u36[i];
// total potential energy
u[i]=(u0[i]+u1[i]+u2[i]+u3[i]+u4[i])*convo;
r[i]=3.98133903-min;
cout<<"\n"<<"distance (in amgstron) :"<<r[i];

30

cout<<"\t"<<"energy (in kJ/mol):"<<u[i];


v=min-incd;
min=v;
}

//storing minimum energy for a particular rotaion in an array


minele=u[0];
mindis=r[0];
for(int j=0;j<=99;j++)
{
if(u[j]<minele)
{
minele=u[j];
mindis=r[j];
}
}
minelement[o]=minele;
mindistance[o]=mindis;
orientation[o]=minangle;

angle=minangle+inc;
minangle=angle;
}
//calculating minimum energy after all possible rotaion along x-axis
mminelement=minelement[0];
mmindistance=mindistance[0];
oorientation=orientation[0];
for(int i=0;i<=1400;i++)
{
if(minelement[i]<mminelement)
{
mminelement=minelement[i];
mmindistance=mindistance[i];
oorientation=orientation[i];
}
}
//finding the coordinates of 5-site methane with minimum orientation position
x1[0][0]=1; x1[1][0]=0; x1[2][0]=0; x1[0][1]=0; x1[1][1]=cos(oorientation); x1[2][1]=-sin(oorientation);
x1[0][2]=0; x1[1][2]=sin(oorientation); x1[2][2]=cos(oorientation);
//coordinate of H1,H2,H3 and H4

31

for(int j=0;j<3;j++)
{
for(int k=0;k<1;k++)
{
newx1[j][k]=0;
newx2[j][k]=0;
newx3[j][k]=0;
newx4[j][k]=0;
for(int l=0;l<3;l++)
{
newx1[j][k]=newx1[j][k]+(x1[j][l]*h1[l][k]);
newx2[j][k]=newx2[j][k]+(x1[j][l]*h2[l][k]);
newx3[j][k]=newx3[j][k]+(x1[j][l]*h3[l][k]);
newx4[j][k]=newx4[j][k]+(x1[j][l]*h4[l][k]);
}
}
}

newxh1=newx1[0][0];
newyh1=newx1[0][1];
newzh1=newx1[0][2]+3.981339030;
newxh2=newx2[0][0];
newyh2=newx2[0][1];
newzh2=newx2[0][2]+3.981339030;
newxh3=newx3[0][0];
newyh3=newx3[0][1];
newzh3=newx3[0][2]+3.981339030;
newxh4=0;
newyh4=0;
newzh4=newx4[0][2]+3.981339030;
cout<<"\n"<<"\n"<<"\n"<<"Minimum energy well after all possible rotation along x-axis =
"<<mminelement<<" kJ/mol";
cout<<"\n"<<"at a distance of = "<<mmindistance<<" amgstrom";
cout<<"\n"<<"for an orientation of= "<<oorientation*(180/3.141592654)<<" degree";
cout<<"\n"<<"\n"<<"and the coordinates of 5-site methane with minimum orientation position is : "<<"\n";
cout<<"\n"<<"c0"<<"\t"<<0<<"\t"<<"\t"<<0<<"\t"<<"\t"<<3.981339;
cout<<"\n"<<"H1"<<"\t"<<newxh1<<"\t"<<newyh1<<"\t"<<"\t"<<newzh1;
cout<<"\n"<<"H2"<<"\t"<<newxh2<<"\t"<<newyh2<<"\t"<<newzh2;
cout<<"\n"<<"H3"<<"\t"<<newxh3<<"\t"<<newyh3<<"\t"<<newzh3;
cout<<"\n"<<"H4"<<"\t"<<newxh4<<"\t"<<"\t"<<newyh4<<"\t"<<"\t"<<newzh4;
//storing the values of coordinates of methane with minimum energy
ofstream fp;
fp.open("x.txt");
fp<<"\n"<<"c0"<<"\t"<<0<<"\t"<<"\t"<<0<<"\t"<<"\t"<<3.981339;
fp<<"\n"<<"H1"<<"\t"<<newxh1<<"\t"<<newyh1<<"\t"<<"\t"<<newzh1;
fp<<"\n"<<"H2"<<"\t"<<newxh2<<"\t"<<newyh2<<"\t"<<newzh2;
fp<<"\n"<<"H3"<<"\t"<<newxh3<<"\t"<<newyh3<<"\t"<<newzh3;
fp<<"\n"<<"H4"<<"\t"<<newxh4<<"\t"<<"\t"<<newyh4<<"\t"<<"\t"<<newzh4;
fp.close();

32

return(0);
}

program 4 : ROTATING THE 5-SITE METHANE MOLECULE ALONG Y-AXIS ABOUT


ITS C-ATOM AND CALCULATING THE MINIMUM ENERGY WELL IN
INTERACTION OF 5-SITE METHANE WITH BENZENE
#include<iostream>
#include<iomanip>
#include<cstdio>
#include<cmath>
#include<fstream>
#include<stdlib.h>
#include<time.h>
#include<limits>

33

using namespace std;


using std::numeric_limits;
int main()
{
float a=59.06865175,b=3.575,c=22.37689,d=3.2,min,mini,max,v,convo,maxangle=(2*3.141592654),angle,
minangle=0,inc,incd;
float xh1,yh1,zh1,newxh1,newyh1,newzh1,xh2,yh2,zh2,newxh2,newyh2,newzh2,xh3,yh3,zh3,newxh3,
newyh3,newzh3,xh4,yh4,zh4,newxh4,newyh4,newzh4;
float r[100],r0[100],u0[100],u1[100],u2[100],u3[100],u4[100],u[100];
float r11[100],r12[100],r13[100],r14[100],r15[100],r16[100],u11[100],u12[100],u13[100],u14[100],
u15[100],u16[100],r21[100],r22[100],r23[100],r24[100],r25[100],r26[100],u21[100],u22[100],u23[100],
u24[100],u25[100],u26[100],r31[100],r32[100],r33[100],r34[100],r35[100],r36[100],u31[100],u32[100],
u33[100],u34[100],u35[100],u36[100],r41[100],r42[100],r43[100],r44[100],r45[100],r46[100],u41[100],
u42[100],u43[100],u44[100],u45[100],u46[100];
float h1[3][1],h2[3][1],h3[3][1],h4[3][1],x[3][3],newx1[3][1],newx2[3][1],newx3[3][1],newx4[3][1];
float minelement[1400],mindistance[1400],minele,mindis,mminelement,mmindistance,orientation[1400],
oorientation;
cout<<"Enter the min and max distance coordinate of benzene from methane ( if carbon of methane is at
coordinate z=3.98 and is above benzene): ";
cin>>mini>>max;
inc=(maxangle-minangle)/1440;
incd=(mini-max)/100;
convo=(1.38*6.022)/1000;

//conversion of unit of energy from K to kJ/mol

//rotation of methane along y-axis about its c-atom


for(int o=0;o<=1400;o++)
{
min=mini;
for(int i=0;i<=99;i++)
{
//interaction of C0 of methane with that of benzene
r0[i]=pow(1.891753667+pow(3.98133903-min,2),0.5);
u0[i]=6*4*a*(pow(b/r0[i],12)-pow(b/r0[i],6));
//coordinates of H4 with origin at centre of C-atom of methane
xh4=0;
yh4=0;
zh4=-1.085524733;
xh1=-0.99995285;
yh1=-0.25602515;
zh1=0.361841577;
xh2=0.718721927;

34

yh2=-0.732812593;
zh2=0.361841577;
xh3=0.275273359;
yh3=0.988837743;
zh3=0.361841577;

h4[0][0]=xh4; h4[1][0]=yh4; h4[2][0]=zh4;


h1[0][0]=xh1; h1[1][0]=yh1; h1[2][0]=zh1;
h2[0][0]=xh2; h2[1][0]=yh2; h2[2][0]=zh2;
h3[0][0]=xh3; h3[1][0]=yh3; h3[2][0]=zh3;
x[0][0]=cos(minangle); x[1][0]=0; x[2][0]=sin(minangle); x[0][1]=0; x[1][1]=1; x[2][1]=0;
x[0][2]=-sin(minangle); x[1][2]=0; x[2][2]=cos(minangle);
for(int j=0;j<3;j++)
{
for(int k=0;k<1;k++)
{
newx4[j][k]=0;
newx1[j][k]=0;
newx2[j][k]=0;
newx3[j][k]=0;
for(int l=0;l<3;l++)
{
newx4[j][k]=newx4[j][k]+(x[j][l]*h4[l][k]);
newx1[j][k]=newx1[j][k]+(x[j][l]*h1[l][k]);
newx2[j][k]=newx2[j][k]+(x[j][l]*h2[l][k]);
newx3[j][k]=newx3[j][k]+(x[j][l]*h3[l][k]);
}
}
}

newxh4=newx4[0][0];
newyh4=newx4[0][1];
newzh4=newx4[0][2]+3.981339030;
newxh1=newx1[0][0];
newyh1=newx1[0][1];
newzh1=newx1[0][2]+3.981339030;
newxh2=newx2[0][0];
newyh2=newx2[0][1];
newzh2=newx2[0][2]+3.981339030;
newxh3=newx3[0][0];
newyh3=newx3[0][1];
newzh3=newx3[0][2]+3.981339030;
//interaction of H4 of methane with that of benzene
r41[i]=pow(pow(newxh4-1.375176933,2)+pow(newyh4+0.025339102,2)+pow(newzh4-min,2),0.5);
r42[i]=pow(pow(newxh4-0.665644160,2)+pow(newyh4+1.203607710,2)+pow(newzh4-min,2),0.5);
r43[i]=pow(pow(newxh4-0.709532773,2)+pow(newyh4-1.178268607,2)+pow(newzh4-min,2),0.5);

35

r44[i]=pow(pow(newxh4+0.709532773,2)+pow(newyh4+1.178268607,2)+pow(newzh4-min,2),0.5);
r45[i]=pow(pow(newxh4+0.665644160,2)+pow(newyh4-1.203607710,2)+pow(newzh4-min,2),0.5);
r46[i]=pow(pow(newxh4+1.375176933,2)+pow(newyh4-0.025339102,2)+pow(newzh4-min,2),0.5);
u41[i]=4*c*(pow(d/r41[i],12)-pow(d/r41[i],6));
u42[i]=4*c*(pow(d/r42[i],12)-pow(d/r42[i],6));
u43[i]=4*c*(pow(d/r43[i],12)-pow(d/r43[i],6));
u44[i]=4*c*(pow(d/r44[i],12)-pow(d/r44[i],6));
u45[i]=4*c*(pow(d/r45[i],12)-pow(d/r45[i],6));
u46[i]=4*c*(pow(d/r46[i],12)-pow(d/r46[i],6));
u4[i]=u41[i]+u42[i]+u43[i]+u44[i]+u45[i]+u46[i];
//interaction of H1 of methane with that of benzene
r11[i]=pow(pow(newxh1-1.375176933,2)+pow(newyh1+0.025339102,2)+pow(newzh1-min,2),0.5);
r12[i]=pow(pow(newxh1-0.665644160,2)+pow(newyh1+1.203607710,2)+pow(newzh1-min,2),0.5);
r13[i]=pow(pow(newxh1-0.709532773,2)+pow(newyh1-1.178268607,2)+pow(newzh1-min,2),0.5);
r14[i]=pow(pow(newxh1+0.709532773,2)+pow(newyh1+1.178268607,2)+pow(newzh1-min,2),0.5);
r15[i]=pow(pow(newxh1+0.665644160,2)+pow(newyh1-1.203607710,2)+pow(newzh1-min,2),0.5);
r16[i]=pow(pow(newxh1+1.375176933,2)+pow(newyh1-0.025339102,2)+pow(newzh1-min,2),0.5);
u11[i]=4*c*(pow(d/r11[i],12)-pow(d/r11[i],6));
u12[i]=4*c*(pow(d/r12[i],12)-pow(d/r12[i],6));
u13[i]=4*c*(pow(d/r13[i],12)-pow(d/r13[i],6));
u14[i]=4*c*(pow(d/r14[i],12)-pow(d/r14[i],6));
u15[i]=4*c*(pow(d/r15[i],12)-pow(d/r15[i],6));
u16[i]=4*c*(pow(d/r16[i],12)-pow(d/r16[i],6));
u1[i]=u11[i]+u12[i]+u13[i]+u14[i]+u15[i]+u16[i];
//interaction of H2 of methane with that of benzene
r21[i]=pow(pow(newxh2-1.375176933,2)+pow(newyh2+0.025339102,2)+pow(newzh2-min,2),0.5);
r22[i]=pow(pow(newxh2-0.665644160,2)+pow(newyh2+1.203607710,2)+pow(newzh2-min,2),0.5);
r23[i]=pow(pow(newxh2-0.709532773,2)+pow(newyh2-1.178268607,2)+pow(newzh2-min,2),0.5);
r24[i]=pow(pow(newxh2+0.709532773,2)+pow(newyh2+1.178268607,2)+pow(newzh2-min,2),0.5);
r25[i]=pow(pow(newxh2+0.665644160,2)+pow(newyh2-1.203607710,2)+pow(newzh2-min,2),0.5);
r26[i]=pow(pow(newxh2+1.375176933,2)+pow(newyh2-0.025339102,2)+pow(newzh2-min,2),0.5);
u21[i]=4*c*(pow(d/r21[i],12)-pow(d/r21[i],6));
u22[i]=4*c*(pow(d/r22[i],12)-pow(d/r22[i],6));
u23[i]=4*c*(pow(d/r23[i],12)-pow(d/r23[i],6));
u24[i]=4*c*(pow(d/r24[i],12)-pow(d/r24[i],6));
u25[i]=4*c*(pow(d/r25[i],12)-pow(d/r25[i],6));
u26[i]=4*c*(pow(d/r26[i],12)-pow(d/r26[i],6));
u2[i]=u21[i]+u22[i]+u23[i]+u24[i]+u25[i]+u26[i];
//interaction of H3 of methane with that of benzene
r31[i]=pow(pow(newxh3-1.375176933,2)+pow(newyh3+0.025339102,2)+pow(newzh3-min,2),0.5);
r32[i]=pow(pow(newxh3-0.665644160,2)+pow(newyh3+1.203607710,2)+pow(newzh3-min,2),0.5);
r33[i]=pow(pow(newxh3-0.709532773,2)+pow(newyh3-1.178268607,2)+pow(newzh3-min,2),0.5);
r34[i]=pow(pow(newxh3+0.709532773,2)+pow(newyh3+1.178268607,2)+pow(newzh3-min,2),0.5);
r35[i]=pow(pow(newxh3+0.665644160,2)+pow(newyh3-1.203607710,2)+pow(newzh3-min,2),0.5);
r36[i]=pow(pow(newxh3+1.375176933,2)+pow(newyh3-0.025339102,2)+pow(newzh3-min,2),0.5);
u31[i]=4*c*(pow(d/r31[i],12)-pow(d/r31[i],6));
u32[i]=4*c*(pow(d/r32[i],12)-pow(d/r32[i],6));
u33[i]=4*c*(pow(d/r33[i],12)-pow(d/r33[i],6));
u34[i]=4*c*(pow(d/r34[i],12)-pow(d/r34[i],6));

36

u35[i]=4*c*(pow(d/r35[i],12)-pow(d/r35[i],6));
u36[i]=4*c*(pow(d/r36[i],12)-pow(d/r36[i],6));
u3[i]=u31[i]+u32[i]+u33[i]+u34[i]+u35[i]+u36[i];
// total potential energy
u[i]=(u0[i]+u1[i]+u2[i]+u3[i]+u4[i])*convo;
r[i]=3.98133903-min;
cout<<"\n"<<"distance (in amgstron) :"<<r[i];
cout<<"\t"<<"energy (in kJ/mol):"<<u[i];
v=min-incd;
min=v;
}

//storing minimum energy for a particular rotaion in an array


minele=u[0];
mindis=r[0];
for(int j=0;j<=99;j++)
{
if(u[j]<minele)
{
minele=u[j];
mindis=r[j];
}
}
minelement[o]=minele;
mindistance[o]=mindis;
orientation[o]=minangle;

angle=minangle+inc;
minangle=angle;
}
//calculating minimum energy after all possible rotaion along y-axis
mminelement=minelement[0];
mmindistance=mindistance[0];
oorientation=orientation[0];
for(int i=0;i<=1400;i++)
{
if(minelement[i]<mminelement)
{
mminelement=minelement[i];
mmindistance=mindistance[i];

37

oorientation=orientation[i];
}
}
//finding the coordinates of 5-site methane with minimum orientation position
x1[0][0]=cos(minangle); x1[1][0]=0; x[2][0]=sin(minangle); x1[0][1]=0; x1[1][1]=1; x1[2][1]=0;
x1[0][2]=-sin(minangle); x1[1][2]=0; x1[2][2]=cos(minangle);
//coordinate of H1,H2,H3 and H4
for(int j=0;j<3;j++)
{
for(int k=0;k<1;k++)
{
newx1[j][k]=0;
newx2[j][k]=0;
newx3[j][k]=0;
newx4[j][k]=0;
for(int l=0;l<3;l++)
{
newx1[j][k]=newx1[j][k]+(x1[j][l]*h1[l][k]);
newx2[j][k]=newx2[j][k]+(x1[j][l]*h2[l][k]);
newx3[j][k]=newx3[j][k]+(x1[j][l]*h3[l][k]);
newx4[j][k]=newx4[j][k]+(x1[j][l]*h4[l][k]);
}
}
}

newxh1=newx1[0][0];
newyh1=newx1[0][1];
newzh1=newx1[0][2]+3.981339030;
newxh2=newx2[0][0];
newyh2=newx2[0][1];
newzh2=newx2[0][2]+3.981339030;
newxh3=newx3[0][0];
newyh3=newx3[0][1];
newzh3=newx3[0][2]+3.981339030;
newxh4=0;
newyh4=0;
newzh4=newx4[0][2]+3.981339030;
cout<<"\n"<<"\n"<<"\n"<<"Minimum energy well after all possible rotation along y-axis =
"<<mminelement<<" kJ/mol";
cout<<"\n"<<"at a distance of = "<<mmindistance<<" amgstrom";
cout<<"\n"<<"for an orientation of= "<<oorientation*(180/3.141592654)<<" degree";
cout<<"\n"<<"\n"<<"and the coordinates of 5-site methane with minimum orientation position is : "<<"\n";
cout<<"\n"<<"c0"<<"\t"<<0<<"\t"<<"\t"<<0<<"\t"<<"\t"<<3.981339;
cout<<"\n"<<"H1"<<"\t"<<newxh1<<"\t"<<newyh1<<"\t"<<"\t"<<newzh1;
cout<<"\n"<<"H2"<<"\t"<<newxh2<<"\t"<<newyh2<<"\t"<<newzh2;

38

cout<<"\n"<<"H3"<<"\t"<<newxh3<<"\t"<<newyh3<<"\t"<<newzh3;
cout<<"\n"<<"H4"<<"\t"<<newxh4<<"\t"<<"\t"<<newyh4<<"\t"<<"\t"<<newzh4;
//storing the values of coordinates of methane with minimum energy
ofstream fp;
fp.open("y.txt");
fp<<"\n"<<"c0"<<"\t"<<0<<"\t"<<"\t"<<0<<"\t"<<"\t"<<3.981339;
fp<<"\n"<<"H1"<<"\t"<<newxh1<<"\t"<<newyh1<<"\t"<<"\t"<<newzh1;
fp<<"\n"<<"H2"<<"\t"<<newxh2<<"\t"<<newyh2<<"\t"<<newzh2;
fp<<"\n"<<"H3"<<"\t"<<newxh3<<"\t"<<newyh3<<"\t"<<newzh3;
fp<<"\n"<<"H4"<<"\t"<<newxh4<<"\t"<<"\t"<<newyh4<<"\t"<<"\t"<<newzh4;
fp.close();
return(0);
}

program 5 : CALCULATING THE MINIMUM ENERGY WELL IN INTERACTION OF 5-SITE

39

METHANE (180 degree i.e, CH up) WITH BENZENE


#include<iostream>
#include<iomanip>
#include<cstdio>
#include<cmath>
#include<fstream>
#include<stdlib.h>
#include<time.h>
#include<limits>
using namespace std;
using std::numeric_limits;
int main()
{
float a=59.06865175,b=3.575,c=22.37689,d=3.2,min,max,v,convo,minangle=3.141592654,incd;
float xh1,yh1,zh1,newxh1,newyh1,newzh1,xh2,yh2,zh2,newxh2,newyh2,newzh2,xh3,yh3,zh3,newxh3,
newyh3,newzh3,xh4,yh4,zh4,newxh4,newyh4,newzh4;
float r[100],r0[100],u0[100],u1[100],u2[100],u3[100],u4[100],u[100];
float r11[100],r12[100],r13[100],r14[100],r15[100],r16[100],u11[100],u12[100],u13[100],u14[100],
u15[100],u16[100],r21[100],r22[100],r23[100],r24[100],r25[100],r26[100],u21[100],u22[100],u23[100],
u24[100],u25[100],u26[100],r31[100],r32[100],r33[100],r34[100],r35[100],r36[100],u31[100],u32[100],
u33[100],u34[100],u35[100],u36[100],r41[100],r42[100],r43[100],r44[100],r45[100],r46[100],u41[100],
u42[100],u43[100],u44[100],u45[100],u46[100];
float h1[3][1],h2[3][1],h3[3][1],h4[3][1],x[3][3],newx1[3][1],newx2[3][1],newx3[3][1],newx4[3][1];
float minele,mindis;
cout<<"enter the min and max distance of benzene from methane ( if carbon of methane is at coordinate
z=3.98 and is above benzene: ";
cin>>min>>max;
incd=(min-max)/100;
convo=(1.38*6.022)/1000;

//conversion of unit of energy from K to kJ/mol

// 180 deg ROTATION OF METHANE ALONG X-AXIS


for(int i=0;i<=99;i++)
{
//interaction of c0 with benzene
r0[i]=pow(1.891753667+pow(3.98133903-min,2),0.5);
u0[i]=6*4*a*(pow(b/r0[i],12)-pow(b/r0[i],6));

//coordinates of H4 with origin at centre of C-atom of methane


xh1=-0.99995285;
yh1=-0.25602515;
zh1=0.361841577;

40

xh2=0.718721927;
yh2=-0.732812593;
zh2=0.361841577;
xh3=0.275273359;
yh3=0.988837743;
zh3=0.361841577;
xh4=0;
yh4=0;
zh4=-1.085524733;
h1[0][0]=xh1; h1[1][0]=yh1; h1[2][0]=zh1;
h2[0][0]=xh2; h2[1][0]=yh2; h2[2][0]=zh2;
h3[0][0]=xh3; h3[1][0]=yh3; h3[2][0]=zh3;
h4[0][0]=xh4; h4[1][0]=yh4; h4[2][0]=zh4;
x[0][0]=1; x[1][0]=0; x[2][0]=0; x[0][1]=0; x[1][1]=cos(minangle); x[2][1]=-sin(minangle);
x[0][2]=0; x[1][2]=sin(minangle); x[2][2]=cos(minangle);
for(int j=0;j<3;j++)
{
for(int k=0;k<1;k++)
{
newx1[j][k]=0;
newx2[j][k]=0;
newx3[j][k]=0;
newx4[j][k]=0;
for(int l=0;l<3;l++)
{
newx1[j][k]=newx1[j][k]+(x[j][l]*h1[l][k]);
newx2[j][k]=newx2[j][k]+(x[j][l]*h2[l][k]);
newx3[j][k]=newx3[j][k]+(x[j][l]*h3[l][k]);
newx4[j][k]=newx4[j][k]+(x[j][l]*h4[l][k]);
}
}
}
//interaction of H4 with benzene
newxh4=newx4[0][0];
newyh4=newx4[0][1];
newzh4=newx4[0][2]+3.981339030;
r41[i]=pow(pow(newxh4-1.375176933,2)+pow(newyh4+0.025339102,2)+pow(newzh4-min,2),0.5);
r42[i]=pow(pow(newxh4-0.665644160,2)+pow(newyh4+1.203607710,2)+pow(newzh4-min,2),0.5);
r43[i]=pow(pow(newxh4-0.709532773,2)+pow(newyh4-1.178268607,2)+pow(newzh4-min,2),0.5);
r44[i]=pow(pow(newxh4+0.709532773,2)+pow(newyh4+1.178268607,2)+pow(newzh4-min,2),0.5);
r45[i]=pow(pow(newxh4+0.665644160,2)+pow(newyh4-1.203607710,2)+pow(newzh4-min,2),0.5);
r46[i]=pow(pow(newxh4+1.375176933,2)+pow(newyh4-0.025339102,2)+pow(newzh4-min,2),0.5);
u41[i]=4*c*(pow(d/r41[i],12)-pow(d/r41[i],6));
u42[i]=4*c*(pow(d/r42[i],12)-pow(d/r42[i],6));
u43[i]=4*c*(pow(d/r43[i],12)-pow(d/r43[i],6));
u44[i]=4*c*(pow(d/r44[i],12)-pow(d/r44[i],6));
u45[i]=4*c*(pow(d/r45[i],12)-pow(d/r45[i],6));
u46[i]=4*c*(pow(d/r46[i],12)-pow(d/r46[i],6));

41

u4[i]=u41[i]+u42[i]+u43[i]+u44[i]+u45[i]+u46[i];
//interaction of H1 with benzene
newxh1=newx1[0][0];
newyh1=newx1[0][1];
newzh1=newx1[0][2]+3.981339030;
r11[i]=pow(pow(newxh1-1.375176933,2)+pow(newyh1+0.025339102,2)+pow(newzh1-min,2),0.5);
r12[i]=pow(pow(newxh1-0.665644160,2)+pow(newyh1+1.203607710,2)+pow(newzh1-min,2),0.5);
r13[i]=pow(pow(newxh1-0.709532773,2)+pow(newyh1-1.178268607,2)+pow(newzh1-min,2),0.5);
r14[i]=pow(pow(newxh1+0.709532773,2)+pow(newyh1+1.178268607,2)+pow(newzh1-min,2),0.5);
r15[i]=pow(pow(newxh1+0.665644160,2)+pow(newyh1-1.203607710,2)+pow(newzh1-min,2),0.5);
r16[i]=pow(pow(newxh1+1.375176933,2)+pow(newyh1-0.025339102,2)+pow(newzh1-min,2),0.5);
u11[i]=4*c*(pow(d/r11[i],12)-pow(d/r11[i],6));
u12[i]=4*c*(pow(d/r12[i],12)-pow(d/r12[i],6));
u13[i]=4*c*(pow(d/r13[i],12)-pow(d/r13[i],6));
u14[i]=4*c*(pow(d/r14[i],12)-pow(d/r14[i],6));
u15[i]=4*c*(pow(d/r15[i],12)-pow(d/r15[i],6));
u16[i]=4*c*(pow(d/r16[i],12)-pow(d/r16[i],6));
u1[i]=u11[i]+u12[i]+u13[i]+u14[i]+u15[i]+u16[i];
//interaction of H2 with benzene
newxh2=newx2[0][0];
newyh2=newx2[0][1];
newzh2=newx2[0][2]+3.981339030;
r21[i]=pow(pow(newxh2-1.375176933,2)+pow(newyh2+0.025339102,2)+pow(newzh2-min,2),0.5);
r22[i]=pow(pow(newxh2-0.665644160,2)+pow(newyh2+1.203607710,2)+pow(newzh2-min,2),0.5);
r23[i]=pow(pow(newxh2-0.709532773,2)+pow(newyh2-1.178268607,2)+pow(newzh2-min,2),0.5);
r24[i]=pow(pow(newxh2+0.709532773,2)+pow(newyh2+1.178268607,2)+pow(newzh2-min,2),0.5);
r25[i]=pow(pow(newxh2+0.665644160,2)+pow(newyh2-1.203607710,2)+pow(newzh2-min,2),0.5);
r26[i]=pow(pow(newxh2+1.375176933,2)+pow(newyh2-0.025339102,2)+pow(newzh2-min,2),0.5);
u21[i]=4*c*(pow(d/r21[i],12)-pow(d/r21[i],6));
u22[i]=4*c*(pow(d/r22[i],12)-pow(d/r22[i],6));
u23[i]=4*c*(pow(d/r23[i],12)-pow(d/r23[i],6));
u24[i]=4*c*(pow(d/r24[i],12)-pow(d/r24[i],6));
u25[i]=4*c*(pow(d/r25[i],12)-pow(d/r25[i],6));
u26[i]=4*c*(pow(d/r26[i],12)-pow(d/r26[i],6));
u2[i]=u21[i]+u22[i]+u23[i]+u24[i]+u25[i]+u26[i];
//interaction of H3 with benzene
newxh3=newx3[0][0];
newyh3=newx3[0][1];
newzh3=newx3[0][2]+3.981339030;
r31[i]=pow(pow(newxh3-1.375176933,2)+pow(newyh3+0.025339102,2)+pow(newzh3-min,2),0.5);
r32[i]=pow(pow(newxh3-0.665644160,2)+pow(newyh3+1.203607710,2)+pow(newzh3-min,2),0.5);
r33[i]=pow(pow(newxh3-0.709532773,2)+pow(newyh3-1.178268607,2)+pow(newzh3-min,2),0.5);
r34[i]=pow(pow(newxh3+0.709532773,2)+pow(newyh3+1.178268607,2)+pow(newzh3-min,2),0.5);
r35[i]=pow(pow(newxh3+0.665644160,2)+pow(newyh3-1.203607710,2)+pow(newzh3-min,2),0.5);
r36[i]=pow(pow(newxh3+1.375176933,2)+pow(newyh3-0.025339102,2)+pow(newzh3-min,2),0.5);
u31[i]=4*c*(pow(d/r31[i],12)-pow(d/r31[i],6));

42

u32[i]=4*c*(pow(d/r32[i],12)-pow(d/r32[i],6));
u33[i]=4*c*(pow(d/r33[i],12)-pow(d/r33[i],6));
u34[i]=4*c*(pow(d/r34[i],12)-pow(d/r34[i],6));
u35[i]=4*c*(pow(d/r35[i],12)-pow(d/r35[i],6));
u36[i]=4*c*(pow(d/r36[i],12)-pow(d/r36[i],6));
u3[i]=u31[i]+u32[i]+u33[i]+u34[i]+u35[i]+u36[i];
// total potential energy due in rotation along x-axis
u[i]=(u0[i]+u1[i]+u2[i]+u3[i]+u4[i])*convo;
r[i]=3.98133903-min;
cout<<"\n"<<"distance (in amgstron) : "<<r[i];
cout<<"\t"<<"energy (in kJ/mol):"<<u[i];
v=min-incd;
min=v;
}

minele=u[0];
mindis=r[0];

//finding the minimum energy well and corresponding distance

for(int j=0;j<=99;j++)
{
if(u[j]<minele)
{
minele=u[j];
mindis=r[j];
}
}
cout<<"\n"<<"\n"<<"\n"<<"Minimum energy well for 0 deg(i.e, CH up) positon of methane = "<<minele<<"
kJ/mol";
cout<<"\n"<<"at a distance of = "<<mindis<<" amgstrom";
ofstream fp;
fp.open("r.txt");
for(int t=0;t<=99;t++)
{
fp<<r[t]<<"\t"<<u[t]<<"\n";
}
fp.close();

//storing the values of distance and energy in a file

return(0);
}

43

program 6 : ROTATING THE 5-SITE METHANE MOLECULE(with CH up) ALONG Z-AXIS


ABOUT ITS C-ATOM AND CALCULATING THE DIFFERENCE BETWEEN MINIMUM AND
MAXIMUM ENERGY WELL IN INTERACTION OF 5-SITE METHANE WITH BENZENE
#include<iostream>
#include<iomanip>
#include<cstdio>
#include<cmath>
#include<fstream>
#include<stdlib.h>
#include<time.h>
#include<limits>
using namespace std;
using std::numeric_limits;
int main()
{
float a=59.06865175,b=3.575,c=22.37689,d=3.2,min,mini,max,v,convo,minangle=0,
maxangle=(2*3.141592654),angle,inc,incd;
float xh1,yh1,zh1,newxh1,newyh1,newzh1,xh2,yh2,zh2,newxh2,newyh2,newzh2,xh3,yh3,zh3,newxh3,
newyh3,newzh3,xh4,yh4,zh4,newxh4,newyh4,newzh4;
float r[100],r0[100],u0[100],u1[100],u2[100],u3[100],u4[100],u[100];
float r11[100],r12[100],r13[100],r14[100],r15[100],r16[100],u11[100],u12[100],u13[100],u14[100],
u15[100],u16[100],r21[100],r22[100],r23[100],r24[100],r25[100],r26[100],u21[100],u22[100],u23[100],
u24[100],u25[100],u26[100],r31[100],r32[100],r33[100],r34[100],r35[100],r36[100],u31[100],u32[100],
u33[100],u34[100],u35[100],u36[100],r41[100],r42[100],r43[100],r44[100],r45[100],r46[100],u41[100],
u42[100],u43[100],u44[100],u45[100],u46[100];
float h1[3][1],h2[3][1],h3[3][1],h4[3][1],x[3][3],x1[3][3],newx1[3][1],newx2[3][1],newx3[3][1],
newx4[3][1];
float minelement[1400],mindistance[1400],minele,mindis,mminelement,mmindistance,
orientation[1400],oorientation,maxe,maxd,maxo;
cout<<"enter the min and max distance of benzene from methane ( if carbon of methane is at coordinate
z=3.98 and is above benzene: ";
cin>>mini>>max;
inc=(maxangle-minangle)/72;
incd=(mini-max)/100;
convo=(1.38*6.022)/1000;

//conversion of unit of energy from K to kJ/mol

// ROTATION OF METHANE ALONG Z-AXIS BY 5 degrees


for(int o=0;o<=72;o++)
{

44

min=mini;
for(int i=0;i<=99;i++)
{
//interaction of c0 with benzene
r0[i]=pow(1.891753667+pow(3.98133903-min,2),0.5);
u0[i]=6*4*a*(pow(b/r0[i],12)-pow(b/r0[i],6));
//coordinates of H4 with origin at centre of C-atom of methane
xh4=0;
yh4=0;
zh4=1.085524733;
xh1=-0.99995285;
yh1=0.25602515;
zh1=-0.361841577;
xh2=0.718721927;
yh2=0.732812593;
zh2=-0.361841577;
xh3=0.275273359;
yh3=-0.988837743;
zh3=-0.361841577;

h1[0][0]=xh1; h1[1][0]=yh1; h1[2][0]=zh1;


h2[0][0]=xh2; h2[1][0]=yh2; h2[2][0]=zh2;
h3[0][0]=xh3; h3[1][0]=yh3; h3[2][0]=zh3;
h4[0][0]=xh4; h4[1][0]=yh4; h4[2][0]=zh4;
x[0][0]=cos(minangle); x[1][0]=-sin(minangle); x[2][0]=0; x[0][1]=sin(minangle);
x[1][1]=cos(minangle); x[2][1]=0; x[0][2]=0; x[1][2]=0; x[2][2]=1;
for(int j=0;j<3;j++)
{
for(int k=0;k<1;k++)
{
newx1[j][k]=0;
newx2[j][k]=0;
newx3[j][k]=0;
newx4[j][k]=0;
for(int l=0;l<3;l++)
{
newx1[j][k]=newx1[j][k]+(x[j][l]*h1[l][k]);
newx2[j][k]=newx2[j][k]+(x[j][l]*h2[l][k]);
newx3[j][k]=newx3[j][k]+(x[j][l]*h3[l][k]);
newx4[j][k]=newx4[j][k]+(x[j][l]*h4[l][k]);
}
}
}
//interaction of H4 with benzene
newxh4=newx4[0][0];
newyh4=newx4[0][1];

45

newzh4=newx4[0][2]+3.981339030;
r41[i]=pow(pow(newxh4-1.375176933,2)+pow(newyh4+0.025339102,2)+pow(newzh4-min,2),0.5);
r42[i]=pow(pow(newxh4-0.665644160,2)+pow(newyh4+1.203607710,2)+pow(newzh4-min,2),0.5);
r43[i]=pow(pow(newxh4-0.709532773,2)+pow(newyh4-1.178268607,2)+pow(newzh4-min,2),0.5);
r44[i]=pow(pow(newxh4+0.709532773,2)+pow(newyh4+1.178268607,2)+pow(newzh4-min,2),0.5);
r45[i]=pow(pow(newxh4+0.665644160,2)+pow(newyh4-1.203607710,2)+pow(newzh4-min,2),0.5);
r46[i]=pow(pow(newxh4+1.375176933,2)+pow(newyh4-0.025339102,2)+pow(newzh4-min,2),0.5);
u41[i]=4*c*(pow(d/r41[i],12)-pow(d/r41[i],6));
u42[i]=4*c*(pow(d/r42[i],12)-pow(d/r42[i],6));
u43[i]=4*c*(pow(d/r43[i],12)-pow(d/r43[i],6));
u44[i]=4*c*(pow(d/r44[i],12)-pow(d/r44[i],6));
u45[i]=4*c*(pow(d/r45[i],12)-pow(d/r45[i],6));
u46[i]=4*c*(pow(d/r46[i],12)-pow(d/r46[i],6));
u4[i]=u41[i]+u42[i]+u43[i]+u44[i]+u45[i]+u46[i];
//interaction of H1 with benzene
newxh1=newx1[0][0];
newyh1=newx1[0][1];
newzh1=newx1[0][2]+3.981339030;
r11[i]=pow(pow(newxh1-1.375176933,2)+pow(newyh1+0.025339102,2)+pow(newzh1-min,2),0.5);
r12[i]=pow(pow(newxh1-0.665644160,2)+pow(newyh1+1.203607710,2)+pow(newzh1-min,2),0.5);
r13[i]=pow(pow(newxh1-0.709532773,2)+pow(newyh1-1.178268607,2)+pow(newzh1-min,2),0.5);
r14[i]=pow(pow(newxh1+0.709532773,2)+pow(newyh1+1.178268607,2)+pow(newzh1-min,2),0.5);
r15[i]=pow(pow(newxh1+0.665644160,2)+pow(newyh1-1.203607710,2)+pow(newzh1-min,2),0.5);
r16[i]=pow(pow(newxh1+1.375176933,2)+pow(newyh1-0.025339102,2)+pow(newzh1-min,2),0.5);
u11[i]=4*c*(pow(d/r11[i],12)-pow(d/r11[i],6));
u12[i]=4*c*(pow(d/r12[i],12)-pow(d/r12[i],6));
u13[i]=4*c*(pow(d/r13[i],12)-pow(d/r13[i],6));
u14[i]=4*c*(pow(d/r14[i],12)-pow(d/r14[i],6));
u15[i]=4*c*(pow(d/r15[i],12)-pow(d/r15[i],6));
u16[i]=4*c*(pow(d/r16[i],12)-pow(d/r16[i],6));
u1[i]=u11[i]+u12[i]+u13[i]+u14[i]+u15[i]+u16[i];
//interaction of H2 with benzene
newxh2=newx2[0][0];
newyh2=newx2[0][1];
newzh2=newx2[0][2]+3.981339030;
r21[i]=pow(pow(newxh2-1.375176933,2)+pow(newyh2+0.025339102,2)+pow(newzh2-min,2),0.5);
r22[i]=pow(pow(newxh2-0.665644160,2)+pow(newyh2+1.203607710,2)+pow(newzh2-min,2),0.5);
r23[i]=pow(pow(newxh2-0.709532773,2)+pow(newyh2-1.178268607,2)+pow(newzh2-min,2),0.5);
r24[i]=pow(pow(newxh2+0.709532773,2)+pow(newyh2+1.178268607,2)+pow(newzh2-min,2),0.5);
r25[i]=pow(pow(newxh2+0.665644160,2)+pow(newyh2-1.203607710,2)+pow(newzh2-min,2),0.5);
r26[i]=pow(pow(newxh2+1.375176933,2)+pow(newyh2-0.025339102,2)+pow(newzh2-min,2),0.5);
u21[i]=4*c*(pow(d/r21[i],12)-pow(d/r21[i],6));
u22[i]=4*c*(pow(d/r22[i],12)-pow(d/r22[i],6));
u23[i]=4*c*(pow(d/r23[i],12)-pow(d/r23[i],6));
u24[i]=4*c*(pow(d/r24[i],12)-pow(d/r24[i],6));
u25[i]=4*c*(pow(d/r25[i],12)-pow(d/r25[i],6));
u26[i]=4*c*(pow(d/r26[i],12)-pow(d/r26[i],6));

46

u2[i]=u21[i]+u22[i]+u23[i]+u24[i]+u25[i]+u26[i];
//interaction of H3 with benzene
newxh3=newx3[0][0];
newyh3=newx3[0][1];
newzh3=newx3[0][2]+3.981339030;
r31[i]=pow(pow(newxh3-1.375176933,2)+pow(newyh3+0.025339102,2)+pow(newzh3-min,2),0.5);
r32[i]=pow(pow(newxh3-0.665644160,2)+pow(newyh3+1.203607710,2)+pow(newzh3-min,2),0.5);
r33[i]=pow(pow(newxh3-0.709532773,2)+pow(newyh3-1.178268607,2)+pow(newzh3-min,2),0.5);
r34[i]=pow(pow(newxh3+0.709532773,2)+pow(newyh3+1.178268607,2)+pow(newzh3-min,2),0.5);
r35[i]=pow(pow(newxh3+0.665644160,2)+pow(newyh3-1.203607710,2)+pow(newzh3-min,2),0.5);
r36[i]=pow(pow(newxh3+1.375176933,2)+pow(newyh3-0.025339102,2)+pow(newzh3-min,2),0.5);
u31[i]=4*c*(pow(d/r31[i],12)-pow(d/r31[i],6));
u32[i]=4*c*(pow(d/r32[i],12)-pow(d/r32[i],6));
u33[i]=4*c*(pow(d/r33[i],12)-pow(d/r33[i],6));
u34[i]=4*c*(pow(d/r34[i],12)-pow(d/r34[i],6));
u35[i]=4*c*(pow(d/r35[i],12)-pow(d/r35[i],6));
u36[i]=4*c*(pow(d/r36[i],12)-pow(d/r36[i],6));
u3[i]=u31[i]+u32[i]+u33[i]+u34[i]+u35[i]+u36[i];
// total potential energy due in rotation along x-axis
u[i]=(u0[i]+u1[i]+u2[i]+u3[i]+u4[i])*convo;
r[i]=3.98133903-min;
v=min-incd;
min=v;
}
//minimum energy for a particular rotaion
minele=u[0];
mindis=r[0];
for(int j=0;j<=99;j++)
{
if(u[j]<minele)
{
minele=u[j];
mindis=r[j];
}
}
minelement[o]=minele;
mindistance[o]=mindis;
orientation[o]=minangle;
//storing the variaation of energy with angle of rotation along z-axis
ofstream fp;
fp.open("z.txt");
for(int t=0;t<=72;t++)
{

47

fp<<orientation[t]*(180/3.141592654)<<"\t"<<minelement[t]<<"\n";
}
fp.close();
angle=minangle+inc;
minangle=angle;
}
mminelement=minelement[0];
mmindistance=mindistance[0];
oorientation=orientation[0];
maxe=minelement[0];
maxd=mindistance[0];
maxo=orientation[0];
//minimum energy after all possible rotaion along z-axis
for(int i=0;i<=72;i++)
{
if(minelement[i]<mminelement)
{
mminelement=minelement[i];
mmindistance=mindistance[i];
oorientation=orientation[i];
}
}
cout<<"\n"<<"\n"<<"\n"<<"Minimum energy well after all possible rotation along z-axis =
"<<mminelement<<" kJ/mol";
cout<<"\n"<<"at a distance of = "<<mmindistance<<" amgstrom";
cout<<"\n"<<"for an orientation of= "<<oorientation*(180/3.141592654)<<" degree";
//maximum energy well among all ipossible rotaion along z-axis
for(int j=0;j<=72;j++)
{
if(minelement[j]>maxe)
{
maxe=minelement[j];
maxd=mindistance[j];
maxo=orientation[j];
}
}
cout<<"\n"<<"\n"<<"\n"<<"Maximum energy well after all possible rotation along z-axis = "<<maxe<<"
kJ/mol";
cout<<"\n"<<"at a distance of = "<<maxd<<" amgstrom";
cout<<"\n"<<"for an orientation of= "<<maxo*(180/3.141592654)<<" degree";
cout<<"\n"<<"\n"<<"The diff in max and min energy well after rotation along z-axis = "<<maxemminelement<<" kJ/mol";
//finding the coordinates of 5-site methane with minimum orientation position
x1[0][0]=cos(oorientation); x1[1][0]=-sin(oorientation); x1[2][0]=0; x1[0][1]=sin(oorientation);
x1[1][1]=cos(oorientation); x1[2][1]=0; x1[0][2]=0; x1[1][2]=0; x1[2][2]=1;

48

//coordinate of H1,H2,H3 and H4


for(int j=0;j<3;j++)
{
for(int k=0;k<1;k++)
{
newx1[j][k]=0;
newx2[j][k]=0;
newx3[j][k]=0;
newx4[j][k]=0;
for(int l=0;l<3;l++)
{
newx1[j][k]=newx1[j][k]+(x1[j][l]*h1[l][k]);
newx2[j][k]=newx2[j][k]+(x1[j][l]*h2[l][k]);
newx3[j][k]=newx3[j][k]+(x1[j][l]*h3[l][k]);
newx4[j][k]=newx4[j][k]+(x1[j][l]*h4[l][k]);
}
}
}
newxh1=newx1[0][0];
newyh1=newx1[0][1];
newzh1=newx1[0][2]+3.981339030;
newxh2=newx2[0][0];
newyh2=newx2[0][1];
newzh2=newx2[0][2]+3.981339030;
newxh3=newx3[0][0];
newyh3=newx3[0][1];
newzh3=newx3[0][2]+3.981339030;
newxh4=0;
newyh4=0;
newzh4=newx4[0][2]+3.981339030;

cout<<"\n"<<"\n"<<"The coordinates of 5-site methane with minimum energy orientation position(i.e, after
rotation by 15 degrees) is : "<<"\n";
cout<<"\n"<<"c0"<<"\t"<<0<<"\t"<<"\t"<<0<<"\t"<<"\t"<<3.981339;
cout<<"\n"<<"H1"<<"\t"<<newxh1<<"\t"<<newyh1<<"\t"<<newzh1;
cout<<"\n"<<"H2"<<"\t"<<newxh2<<"\t"<<newyh2<<"\t"<<newzh2;
cout<<"\n"<<"H3"<<"\t"<<newxh3<<"\t"<<newyh3<<"\t"<<newzh3;
cout<<"\n"<<"H4"<<"\t"<<newxh4<<"\t"<<"\t"<<newyh4<<"\t"<<"\t"<<newzh4;
//storing the values of coordinates of methane with minimum energy
ofstream fp;
fp.open("z1.txt");
fp<<"\n"<<"c0"<<"\t"<<0<<"\t"<<"\t"<<0<<"\t"<<"\t"<<3.981339;
fp<<"\n"<<"H1"<<"\t"<<newxh1<<"\t"<<newyh1<<"\t"<<newzh1;
fp<<"\n"<<"H2"<<"\t"<<newxh2<<"\t"<<newyh2<<"\t"<<newzh2;
fp<<"\n"<<"H3"<<"\t"<<newxh3<<"\t"<<newyh3<<"\t"<<newzh3;
fp<<"\n"<<"H4"<<"\t"<<newxh4<<"\t"<<"\t"<<newyh4<<"\t"<<"\t"<<newzh4;
fp.close();

49

return(0);
}

References

Vinays thesis, Role of functional groups on adsorption of methane and carbon dioxide in
activated carbons (2011).

Ashley, L., Figgs, M., Sinnokrot, M. and Sherrill, C. (2006) Aliphatic CH/ interactions:
Methane-benzene, methane-phenol, and methane-indole complexes.
Allen_M._P.,_Tildesley_D._J._Computer_simulation_of_liquids_(1987).
ADSORBED NATURAL GAS STORAGE WITH ACTIVATED CARBON,
Jian Sun, Todd A. Brady and Mark J. Rood
Department of Civil Engineering, University of Illinois
205
rth Mathews Ave., Urbana, IL 61801
Methane storage: Adsorption fundamentals and preparation of an ideal carbonaceous
adsorbent, Dr. Alain Celzard_Professor at the University Henri Poincar of Nancy, France.

Archer, D. (2006) Global Warming: Understanding the Forecast. Wiley-Blackwell,


first edition.

Boys, S. and Bernardi, F. (1970) The calculation of small molecular interactions by the
differences of separate total energies. Some procedures with reduced errors.
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