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Department of Chemical Engineering
National Institute of Technology
Calicut 673601 (India)

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 methane–benzene 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.


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......................................................................................................


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.............................................................................................


Appendix A
Appendix B


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.
M85 (85% methanol in gasoline)
M 100 ( 100% methanol)
LPG (Liquefied petroleum gas)

g of O3/mile

 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
HCs (non-methane)

% Reduction

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.


ions. One of the main disadvantages of zeolites is that their surface area cannot be increased beyond a certain limit (1000 m 2/g). 3. these materials are still being researched on laboratory scale. or dissolved solid to a surface. 1. the gas from the bulk gets adsorbed onto the surface of the adsorbent under the influence of attractive surface forces. 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. This can happen in two ways: by chemisorption. The size and shape of the pores along with the type of material. However. Unlike zeolites and MOFs. 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. composed of both inorganic and organic building blocks. adsorbed natural gas (ANG): In the ANG process. 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. 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. they are hydrophilic and hence their performance may be reduced in the presence of water. The linker molecules are organic which may be functionalized with various functional groups. where the chemical nature of the gas (adsorbate) does not change. Zeolites are naturally occurring aluminosilicates. In addition to this. liquid. Their topology consists of a network of interconnecting channels and/or cages. Modifications are mainly done by attaching functional groups on the linker molecules and studying their effect on gas uptake. Presently. 1. 2. Zeolites. Adsorbents are highly micro porous materials with very high surface area. carbons and metal organic frameworks have pore dimensions of the order of molecular size. ANG has the lowest volumetric energy density among the storage methods. which involves breaking/formation of chemical bonds and physisorption. Metal organic frameworks are novel materials in this field of gas storage. pore size etc. In the process of adsorption. or molecules from a gas. the gas is stored in an adsorbed state in a micro porous adsorbent material. affects its performance. As the values ( in table 4) indicates.3 Adsorbent materials Adsorption is the adhesion of atoms. It is a surface phenomenon and is a consequence of surface energy. In order for ANG to achieve an energy density equal to that of the commercialized CNG system. They have cagelike structure made up of metal-atom-cores linked with organic linker molecules. they have distribution in the pore size and 6 . zeolites with high silicon content are hydrophobic and hence may be helpful where water is hindering the adsorption process. Activated carbons are another class of potential adsorbents in this area.3. MOFs have the ability to adsorb huge quantities of CH4 . as they have very high surface area.The ease with which their chemical composition can be varied by modifying their synthesis techniques makes them very attractive for research. This process creates a film of the adsorbate on the surface of the adsorbent. Hence choosing an adsorbent for a particular application will depend mainly on these factors. characterized by very large pores. the US Department of Energy has set the target for storage density as 180 V/V. The success of the adsorption capture/separation process depends a lot on the nature of the adsorbent material. However it has the potential to be one of the least expensive depending on the type of adsorbent material.

coals etc.shapes. Apart from adsorption. 7 . Adsorbent T (K) Amount adsorbed ( Mmolg-1 ) NaX 298 66 NaY 298 56 CaX 298 82 298 44 PX-21. Hence fictionalization of materials in order to obtain certain specific characteristics is an active area of research in the field of synthetic chemistry. hydrogen bond donors and acceptors are collectively termed as functional groups. and defects on the material. Table 3: Adsorbent materials for methane adsorption at 35 bar. The activated carbons have an advantage over zeolites in terms of hydrophobicity and also can attain very high surface area. Certain sites on the material preferentially adsorb gases more than others and are referred to as adsorption or binding sites. Compared to MOFs. These sites may be functional groups. etc. the activated carbons are less expensive to produce. Location of the adsorption sites on the material depends on its structure and chemistry. functional groups play important roles in other applications like catalysis. The strength of these materials lies in the fact that they can be prepared from less expensive precursor materials like coconut shell. Hence careful consideration needs to be give to the chemistry and structure while choosing an adsorbent for certain application. drug delivery and nanotechnology. acids. 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. corn grain. fruit stones. bases. Metal atoms. nucleophiles.

1. 6-12 potential. V is the intermolecular potential between the two atoms or molecules. ε and σ are called as LJ parameters and they depends on the nature of molecules present for interaction. models the repulsion between atoms when they are 8 . and r is the distance of separation between both particles (measured from the centre of one particle to the centre of the other particle). dominating at short distance. A form of the potential was first proposed in 1924 by Sir John Edward Lennard-jones. Where. σ is the distance at which the intermolecular potential between the two particles is zero.  Lennard-Jones Potential The Lennard-Jones potential (also referred to as the L-J potential. It gives a measurement of how close two nonbonding particles can get and is thus referred to as the van der waals radius. or 12-6 potential) is a mathematically simple model that approximates the interaction between a pair of neutral atoms or molecules.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. −12 The term r . Figure 1: Lennard-Jones potential curve with parameters. ε is the depth of the potential well and a measure of how strongly the two particles attract each other. generally referred as Lennard-Jones separation distance.

if we keep pushing the two bound particles together passed their equilibrium distance. the probability of interaction increases. dominating at large distance. as particles are so close to each other that their electrons are forced to occupy each other’s orbital. In fact. on physical grounds an exponential behaviour would be more appropriate. 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. the distance between their centres will continue to decrease until the particles reach an equilibrium. we can say that their bonding potential energy is zero. 9 . repulsion occurs as each particle attempts to retain the space in their respective orbital. their bonding potential energy rises rapidly as the distance of separation between them decreases below the equilibrium distance. This is the term which −6 gives cohesion to the system. Bonding Potential As mentioned earlier. For the sake of simplicity then. originated by dipole-dipole interactions in turn due to fluctuating dipoles. Now.brought very close to each other. which is specified by the separation distance at which the minimum potential energy is reached. However. When two nonbonding particles are an infinite distance apart. The exponent 12 was chosen exclusively on a practical basis. the Lennard-Jones Potential is a function of the distance between the centres of two particles. A r attraction is originated by Van der Waals dispersion forces. While the particles are bound. Therefore. repulsion begins to occur. the energy of the system increases abruptly. constitute the attractive part. as the distance of separation decreases. −6 The term r . Its physical origin is related to the Pauli principle: when the electronic cloud surrounding the atoms starts to overlap. the possibility of them coming together and interacting is minimal. Despite the repulsive force between both particles.

At this point. However. Lastly. as the separation between the two particles reaches a distance slightly greater than σ. the pair of atoms or molecules experiences a small stabilizing force.Figure 2: The interaction phenomenon can be view as two spherical balls separated by distance r. the pair of particles is most stable and will remain in that orientation until an external force is exerted upon them. the potential energy is negative and approaches zero as the separation distance increases to infinity (force is attractive). As the separation distance decreases below equilibrium the potential energy becomes increasingly positive (force is repulsive). 10 . 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. This indicates that at such long-range distances. Such a large potential energy is energetically unfavourable as it indicates an overlapping of atomic orbital. the potential energy reaches a minimum value (force is zero). at long separation distances.

Figure 3: Lennard-Jones potential curve with forces. 11 .  Coulombic Potential The Lennard--Jones potential is one important part of the interaction between two molecules. q1 and q2 are the electric charge in coulombs carried by charge 1 and 2 respectively. The resulting potential is shown in Figure 4. It acts along the line connecting the two charges. The Coulomb potential is an effective pair potential that describes the interaction between two point charges. Interactions between two molecules due to their permanent dipole moments are described approximately by treating the charged portions of the molecule as point charges. both are positive or both are negative) the potential is repulsive.e. The second part of the interaction is due to forces between electrical charges and is called by coulombic potential. It is given by the equation: where r is the distance between two ions. Two oppositely charged particles will give an attractive potential. whereas if both particles are of the same sign (i. and ε0 is the electrical permittivity of space..

a rotation matrix is a matrix that is used to perform a rotation in Euclidean space.e. y. For example the matrix rotates points in the xy-Cartesian plane counterclockwise through an angle θ about the origin of the Cartesian coordinate system. Since matrix multiplication has no effect on the zero vector (i.Figure 4: The Coulomb potential. To perform the rotation using a rotation matrix R.5 Rotation Matrices In linear algebra. or z axis. the position of each point must be represented by a column vector v. The following three basic rotation matrices rotate vectors about the x. rotation matrices can only be used to describe rotations about the origin of the coordinate system. The bottom curve represents the interaction between two particles of opposite charge. on the coordinates of the origin). A rotated vector is obtained by using the matrix multiplication Rv. 1. in three dimensions: 12 . the top curve represents the interaction of particles of equal charge.. containing the coordinates of the point.

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

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.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.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. We need to find the minimum possible well in case of methane benzene system in order to check its most stable orientation. 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. 2. namely the one-site and Kollman five-site models. Both the models successfully reproduce the fluid-phase behaviour of 14 . There are two widely used classical models for methane.

901 -0.3 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.4 2.0 Five-site model C H C H C H 3.73 ε (K) 148 q (e) 0. 15 . 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. Table 4 : Lennard-Jones parameters and Coulombic charges for one-site and five-site methane models. σ (A) One-site model 3.055 7. The charges and the LJ parameters for the two models are shown in the Table 3.methane.65 55.165 2. Both the five-site and one-site models are depicted in the Figure 5.66 0.

and ε0 is a constant called the permittivity of free space.. q2 are Coulombic charges of the interacting sites.2 ε1. with 1 hydrogen atom attached to each carbon atom. evaluated using equation 2...0 0..2 is the effective Lennard-Jones diameter.. q1 .0 2.... benzene is classed as a hydrocarbon.. which are modeled as a sum of Lennard-Jones and Coulombic potential energies. The interaction between sites 1 and 2 on the molecules...2 is the effective well depth. Table 5: Lennard-Jones parameters and Coulombic charges for Benzene model.3541 0.. Because its molecules contain only carbon and hydrogen atoms..2 is the distance between the interacting sites. are given as .75 0. 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.0 55. σ (A) ε (K) q (e) C H C H C H Benzene 3. The effective Lennard-Jones diameter and well-depth for interaction between two different species is given by the Lorentz-Berthelot mixing rule 16 .Benzene is an organic chemical compound with the molecular formula C6H6.3 r1. evaluated using equation 2....1 where σ1..0 0... 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...4 Interactions The interactions are between methane molecules and benzene. 2. Its molecule is composed of 6 carbon atoms joined in a ring..

............. as the 17 .... Figure 7 : Potential energy curve for 1-site methane model over benzene................................... The curve obtained through this program is shown in figure 7...... 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............ εi is the well depth for the ith species...... In this system also only Lennard-Jones interaction is there......98 angstrom which matches with the Vinay's thesis (IISc Bangalore)..................... 2................6 kJ/mol at a seperation of 3....2............................3 where σi is the Lennard-Jones diameter for the ith species....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............2......... But in case of five-site methane the calculation of minimum energy well is much more complicated as compared to the previous system............... The minimum potential energy well obtained in this case is around -4. 1........ 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......

but this system gives different potential energy well for different orientation with respect to benzene ring.15 angstroms. So in order to find the minimum potential well for five-site methane-benzene system. Figure 8: Initial orientation of 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.using the equation where the Lennard-Jones parameters for five-site methane is given in table 4 and for benzene in table 5. 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). not like that in case of one-site methane which gives only a single minimum potential well. I started calculating the interaction potential from the initial orientation of methane benzene system given to me shown in figure 8. I proceed through following steps to find the minimum potential well for five-site methanebenzene system. The curve obtained is shown in figure 9. to find the minimum energy well among all orientation possible and corresponding separation. The minimum potential energy well obtained in this case is around -4. Many small programs are written to plot the potential energy curve.385 kJ/mol at a separation of 4.coulombic part is zero for methane-benzene system. 1. The coordinates of initial five-site methane and benzene is given in coordinate-2 and coordinate-1 (in appendix A) respectively. 18 .

Figure 10: Most stable configuration after rotating the five-site methane molecule about its centre of mass along x and y-axis 3. 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). 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. This is done by writing program 5 (appendix B) using the coordinates of five-site methane molecule with CH-up and benzene from the 19 . Calculating the value of minimum energy well by plotting potential energy curve for the orientation of methane with CH-up shown in figure. 2. 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.Figure 9: Potential energy curve for 5-site methane model (CH down) over benzene. 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.

Figure 12: Variation of energy with rotation along z-axis 2. 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 curve obtained is shown in figure 11. The difference in energy well is merely 0. These values matches with Vinay's thesis and CCSD (T) (Tsuzuki et al. 20 .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. 2000. Figure 11: Potential energy curve for 5-site methane model (CH up) over benzene... Ashley et al.0663 kJ/mol. This the minimum potential energy well in five-site methane and benzene interaction. about its centre of mass along z-axis. 4. Like for initial orientation of methane.0643 kJ/mol at a separation of 3. where potential energy curves for both orientation has been compared.74 angstroms.coordinate-3 and coordinate-1(appendix A). where energy is plotted against the degree of rotation along z-axis. 2006) but the orientation doesn't.0031 kJ/mol shown in figure 12. The minimum energy orientation is shown in figure 15 and corresponding energy well is -6. 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 minimum potential energy well obtained in this case comes out to be around -6. Rotating the five-site methane molecule (with CH-up) shown in figure 10.

21 .Figure 13: Comparison of potential curves for 5-site methane over benzene with its CH-up and CH-down orientation. 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 10.0663 kJ/mol and corresponding interatomic distance of 3. 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. with minimum energy well of -6.74 angstroms.

375176933 0.445067955 2.993995285 0.045052983 -0.817565247 -0.256025150 -0.094964472 2.025339102 -1.665644160 -1.275273359 0.094964472 -1.817565256 -0.445067955 -0.817565247 -0.732812593 0.045052983 -0.261551005 -1.61950 22 .000000 -0.817565265 -0.817565265 -0.203607710 -2.709532773 1.343180607 2.709532773 -0.817565256 -0.817565256 coordinates 2-Initial coordinates of 5-site methane C0 H1 H2 H3 H4 0.000000 0.343180607 4.343180607 4.817565256 -0.895814297 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 0.665644160 0.98134 3.000000000 -0.988837743 0.178268607 1.999953 0.817565256 -0.718721927 0.261551005 -0.203607710 1.183516950 1.000000000 0.817565256 -0.000000000 3.817565265 -0.178268607 -2.140017455 0.981339030 4.183516950 -1.817565247 -0.000000000 -0.Appendix A coordinates 1-coordinates of benzene C1 C2 C3 H H C4 C5 H H C6 H H 1.375176933 -2.256030 3.140017455 2.025339102 0.

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 0.022)/1000.06686 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.506108 0.000000 3.718722 0.02639 0.521824 -1. float r[100].000000 -0.38*6.61950 3.H2 H3 H4 0.61948 5.988832 0.000000 0.61950 3.732818 0.3222. float minele. cout<<"Enter the min and max distance of methane centre from benzene centre in amgstrom : ".c.mindis.000000 0.61948 5.u[100].61950 5.718722 -0.0000000 -0.275273 0.61950 3. //conversion of unit of energy from K to kJ/mol 23 .61951 3.000000 0.0000000 0. int main() { float a=92.256030 -0.min.8838980 0.732818 -0.max.b=3.v[100].98134 3.899616 0. c=(1. using 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 0.74.000000 0.h> #include<time.0099636 0.h> #include<limits> using namespace std.275273 0.000000 3. cin>>min>>max.61951 3.98134 3.988832 0.999953 -0.000000 3.

} minele=u[0].6)).j<=90. min=v[i+1].2)+pow(min. mindis=v[j]. for(int i=0. ofstream fp. } 24 .2)).i<=99. cout<<"\t"<<"Energy (in kJ/mol):"<<u[i].j++) { if(u[j]<minele) { minele=u[j].open("one. cout<<"\n"<<"at a distance of = "<<mindis<<" amgstrom ".5). v[i+1]=min+inc.12)-pow(b/r[i]. // storing the values of distance and energy in a file return(0).0. u[i]=c*6*4*a*(pow(b/r[i]. v[0] for(int j=0.3754.j<=99. } } cout<<"\n"<<"\n"<<"\n"<<"Minimum energy well = "<<minele<<" kJ/mol ".i++) //finding energy corresponds to different seperation distance { r[i]=pow((pow(1. mindis=v[0].close(). } fp. fp. //finding the minimum energy well and corresponding distance for(int j=0.j++) { fp<<v[j]<<"\t"<<u[j]<<"\n".txt"). cout<<"\n"<<"Distance (in amgstron) : "<<min.

r16[100].h> #include<time.r15[100]. p=(1. int main() { float a=59.r11[100].u16[100].v.38*6.r14[100].c=22.max.i< CH down) WITH BENZENE #include<iostream> #include<iomanip> #include<cstdio> #include<cmath> #include<fstream> #include<stdlib.u14[100].022)/1000. using std::numeric_limits.u13[100].u12[100].37689. float minele. cin>>min>>max.b=3.program 2 : CALCULATING THE MINIMUM ENERGY WELL IN INTERACTION OF 5SITE METHANE (0 degree i.u4[100].u1[100].r12[100]. float r[100].u15[100].575.e.h> #include<limits> using namespace std. u11[100].2.06865175.i++) //finding energy corresponds to different seperation distance is 25 .r0[100]. //conversion of unit of energy from K to kJ/mol for(int i=0.u0[100].98 and is above benzene): ". cout<<"Enter the min and max distance coordinate of benzene from methane ( if carbon of methane at coordinate z=3.r4[100].min.r13[100].x.d=3. inc=((min-max)/100).u[100].

12)-pow(d/r14[i].12)-pow(d/r15[i]. u14[i]=4*c*(pow(d/r14[i]. mindis=r[0].98133903-min. u11[i]=4*c*(pow(d/r11[i].0.5). mindis=r[j]. u4[i]=6*4*c*(pow(d/r4[i]. //interaction of H1 of methane with C of benzene x=pow(4.0.5).12)-pow(d/r11[i].5). r15[i]=pow(2.6)).6)).0.j<=99. u16[i]=4*c*(pow(d/r16[i]. u1[i]=3*(u11[i]+u12[i]+u13[i]+u14[i]+u15[i]+u16[i]). u12[i]=4*c*(pow(d/r12[i]. v=min-inc. u15[i]=4*c*(pow(d/r15[i]. u13[i]=4*c*(pow(d/r13[i].895814297-min.2). u0[i]=6*4*a*(pow(b/r0[i].2).12)-pow(d/r13[i].2314411546+x. } 26 .343180607-min.j++) { if(u[j]<minele) { minele=u[j]. //finding the minimum energy well and corresponding distance for(int j=0.67212611+x.0. r[i]=3.12)-pow(d/r12[i].{ //interaction of C0 of methane with that of benzene r0[i]=pow(1.5).0. } minele=u[0].5).2).891753667+pow(3. //total potential enegy u[i]=p*(u0[i]+u1[i]+u4[i]). r13[i]=pow(4. cout<<"\n"<<"Distance (in amgstron) : "<<r[i]. cout<<"\t"<<"Energy (in kJ/mol):"<<u[i].12)-pow(d/r4[i].694457539+x.979539677+x.891753667+pow(2.6)).5). r12[i]=pow(3. r14[i]=pow(0.6)).6)).5).0.0. r11[i]=pow(5. //interaction of H4 of methane with C of benzene r4[i]=pow(1.0.6)).12)-pow(d/r16[i].6)). min=v.6)).934876815+x.12)-pow(b/r0[i]. r16[i]=pow(0.242290386+x.98133903-min.5).

yh2.newxh3. fp.} cout<<"\n"<<"\n"<<"\n"<<"Minimum energy well for 0 deg(i.newxh4. //storing the values of distance and energy in a file return(0).u3[100].37689.angle. 27 . } 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.xh2.v.zh4.zh1.newzh1.txt").h> #include<time.j<=99.newzh4.convo. ofstream fp.newxh2.e.r0[100].u1[100]> #include<limits> using namespace"five.yh3. newyh3.141592654) cout<<"\n"<<"at a distance of = "<<mindis<<" amgstrom". for(int j=0. CH down) positon of methane = "<<minele<<" kJ/mol".min.maxangle=(2*3.newyh4.xh3. int main() { float a=59. float r[100].newxh1.zh2.incd.yh1. using std::numeric_limits.d=3.u4[100].newyh1.xh4.j++) { fp<<r[j]<<"\t"<<u[j]<<"\n".max.06865175. minangle=0.c=22. } fp. float xh1.u[100].u2[100].u0[100].

r46[100].mmindistance.i<=99.u34[100].u43[100].orientation[1400].h2[3][1].u11[100].r33[100].r43[100]. h2[2][0]=zh2. h4[0][0]=xh4.u25[100]. zh3=0.r31[100].085524733. //coordinates of H4 with origin at centre of C-atom of methane xh4=0.r32[100].25602515.u36[100]. yh1=-0.r41[100]. h3[1][0]=yh3. xh1=-0.mminelement.u26[100].u22[100].r15[100].2).r26[100]. zh4=-1.718721927.r24[100].6)).o<=1400.r42[100].r25[100].u14[100].98 and is above benzene): ".98133903-min.newx3[3][1]. yh4=0.h3[3][1].988837743.u44[100]. 28 . yh3=0. u42[100].r12[100].u35[100]. for(int i=0.i++) { //interaction of C0 of methane with that of benzene r0[i]=pow(1. xh2=0.r45[100].5).38*6.r34[100].r23[100].u31[100]. incd=(mini-max)/100.r44[100]. u15[100]. zh1=0.12)-pow(b/r0[i].newx1[3][1]. //conversion of unit of energy from K to kJ/mol //rotation of methane along x-axis about its c-atom for(int o=0.x[3][3]. h3[0][0]=xh3.u12[100].u41[100].mindistance[1400].r13[100].u23[100].r14[100].891753667+pow(3. float minelement[1400].float r11[100]. u24[100].u13[100].newx2[3][1]. zh2=0.r22[100].h4[3][1].732812593.r36[100].99995285. h1[2][0]=zh1.mindis.u45[100]. u33[100]. xh3=0.361841577.o++) { min=mini.u46[100]. cout<<"Enter the min and max distance coordinate of benzene from methane ( if carbon of methane is at coordinate z=3.275273359. float h1[3][1].newx4[3][1].u32[100].minele. yh2=-0. convo=(1.0. h4[1][0]=yh4.u16[100]. u0[i]=6*4*a*(pow(b/r0[i].022)/1000. inc=(maxangle-minangle)/1440.r35[100]. h2[1][0]=yh2. h3[2][0]=zh3.r21[100].r16[100].361841577. h4[2][0]=zh4. h1[1][0]=yh1.u21[100]. h2[0][0]=xh2.361841577. cin>>mini>>max. oorientation. h1[0][0]=xh1.

5).2). u42[i]=4*c*(pow(d/r42[i]. 29 .375176933.981339030.6)).2)+pow(newzh4-min. r45[i]=pow(pow(newxh4+0.203607710. newxh2=newx2[0][0]. r46[i]=pow(pow(newxh4+1.2)+pow(newyh4-1.2)+pow(newzh4-min. x[1][1]=cos(minangle).12)-pow(d/r45[i].l<3.2)+pow(newzh4-min.6)).2)+pow(newzh4-min.k++) { newx4[j][k]=0.6)).709532773. newx1[j][k]=0. x[1][2]=sin(minangle).12)-pow(d/r43[i].j<3.2). newzh2=newx2[0][2]+3.6)). newyh4=newx4[0][1].709532773.5). newxh1=newx1[0][0].12)-pow(d/r44[i].l++) { newx4[j][k]=newx4[j][k]+(x[j][l]*h4[l][k]). r42[i]=pow(pow(newxh4-0. x[2][1]=-sin(minangle).j++) { for(int k=0. for(int j=0.6)).12)-pow(d/r41[i]. newyh3=newx3[0][1]. u41[i]=4*c*(pow(d/r41[i].665644160. u43[i]=4*c*(pow(d/r43[i].12)-pow(d/r42[i].0. newx1[j][k]=newx1[j][k]+(x[j][l]*h1[l][k]). //interaction of H4 of methane with that of benzene r41[i]=pow(pow(newxh4-1. u44[i]=4*c*(pow(d/r44[i]. newx3[j][k]=0. newx3[j][k]=newx3[j][k]+(x[j][l]*h3[l][k]).5).6)). newyh2=newx2[0][1]. newzh1=newx1[0][2]+3.981339030.2)+pow(newzh4-min.665644160.0.025339102.2)+pow(newyh4+0.2).12)-pow(d/r46[i]. r43[i]=pow(pow(newxh4-0. r44[i]=pow(pow(newxh4+0. newxh3=newx3[0][0].2). newzh4=newx4[0][2]+3.2)+pow(newyh4+1.375176933.0.981339030. for(int l=0.0. x[0][1]=0.2).2)+pow(newyh4-1. x[2][0]=0.2)+pow(newyh4+1.2)+pow(newzh4-min. newzh3=newx3[0][2]+3. newyh1=newx1[0][1].0.2)+pow(newyh4-0.178268607. x[1][0]=0. u46[i]=4*c*(pow(d/r46[i].2).203607710. u45[i]=4*c*(pow(d/r45[i].k<1. } } } newxh4=newx4[0][0]. x[2][2]=cos(minangle).5).5).178268607.981339030. newx2[j][k]=0.5).025339102. u4[i]=u41[i]+u42[i]+u43[i]+u44[i]+u45[i]+u46[i].x[0][0]=1.0. x[0][2]=0. newx2[j][k]=newx2[j][k]+(x[j][l]*h2[l][k]).

r26[i]=pow(pow(newxh2+1.5). 30 .025339102. r36[i]=pow(pow(newxh3+1.2)+pow(newyh1-1.2).12)-pow(d/r15[i].12)-pow(d/r31[i].2). u24[i]=4*c*(pow(d/r24[i].2)+pow(newzh3-min. u2[i]=u21[i]+u22[i]+u23[i]+u24[i]+u25[i]+u26[i].6)).6)).2)+pow(newzh3-min.12)-pow(d/r34[i].12)-pow(d/r13[i].2)+pow(newzh3-min.2).709532773.0.2)+pow(newyh1+0.6)).2)+pow(newyh3-0.98133903-min.2)+pow(newzh2-min.2)+pow(newyh1-1. cout<<"\n"<<"distance (in amgstron) :"<<r[i].2).375176933.6)).12)-pow(d/r35[i].12)-pow(d/r11[i].2)+pow(newyh3-1. u31[i]=4*c*(pow(d/r31[i].2).2).5).2)+pow(newzh2-min. u14[i]=4*c*(pow(d/r14[i].12)-pow(d/r24[i].709532773.2).0.2)+pow(newyh1-0. r13[i]=pow(pow(newxh1-0.665644160.0. u26[i]=4*c*(pow(d/r26[i].12)-pow(d/r12[i]. u11[i]=4*c*(pow(d/r11[i].2)+pow(newyh3+1.0. u23[i]=4*c*(pow(d/r23[i].0. u21[i]=4*c*(pow(d/r21[i]. r34[i]=pow(pow(newxh3+0.5).2)+pow(newzh1-min.6)).2).203607710.2)+pow(newzh3-min.709532773.12)-pow(d/r25[i].12)-pow(d/r33[i].2).375176933. r32[i]=pow(pow(newxh3-0. u35[i]=4*c*(pow(d/r35[i].0.025339102.2)+pow(newzh1-min.6)).12)-pow(d/r32[i].5).5).0.2)+pow(newzh2-min.2)+pow(newzh2-min.12)-pow(d/r22[i].5).2).2).375176933.6)).178268607. u34[i]=4*c*(pow(d/r34[i].2)+pow(newzh3-min. r35[i]=pow(pow(newxh3+0.5).665644160.2)+pow(newyh2+0. r16[i]=pow(pow(newxh1+1.203607710. //interaction of H2 of methane with that of benzene r21[i]=pow(pow(newxh2-1.709532773. r[i]=3.12)-pow(d/r14[i].2).6)).375176933. r33[i]=pow(pow(newxh3-0.5).5).178268607.2)+pow(newyh2-1.5).0.12)-pow(d/r23[i].2)+pow(newyh3+1. u16[i]=4*c*(pow(d/r16[i].2).665644160.2). u32[i]=4*c*(pow(d/r32[i].0.2).375176933.6)).5).5).2)+pow(newyh2-0. u15[i]=4*c*(pow(d/r15[i].6)).12)-pow(d/r26[i]. r22[i]=pow(pow(newxh2-0.025339102.0.203607710.//interaction of H1 of methane with that of benzene r11[i]=pow(pow(newxh1-1.2)+pow(newyh1+1. u22[i]=4*c*(pow(d/r22[i]. r23[i]=pow(pow(newxh2-0.2).2)+pow(newyh1+1.2)+pow(newzh1-min.5). r15[i]=pow(pow(newxh1+0.6)). u12[i]=4*c*(pow(d/r12[i].665644160.665644160.0.5). r24[i]=pow(pow(newxh2+0.203607710. u33[i]=4*c*(pow(d/r33[i]. r25[i]=pow(pow(newxh2+0.203607710.6)).0.12)-pow(d/r21[i].0.2)+pow(newzh3-min.6)).6)).178268607. u25[i]=4*c*(pow(d/r25[i]. u36[i]=4*c*(pow(d/r36[i].12)-pow(d/r16[i].665644160.6)).2)+pow(newzh2-min.2)+pow(newyh3+0.5). //interaction of H3 of methane with that of benzene r31[i]=pow(pow(newxh3-1.2).2). u13[i]=4*c*(pow(d/r13[i].0.0.5).178268607. u1[i]=u11[i]+u12[i]+u13[i]+u14[i]+u15[i]+u16[i].0.12)-pow(d/r36[i].025339102. u3[i]=u31[i]+u32[i]+u33[i]+u34[i]+u35[i]+u36[i].709532773.6)).5).2)+pow(newzh1-min. r12[i]=pow(pow(newxh1-0.2)+pow(newzh1-min.6)).2)+pow(newyh3-1.2)+pow(newyh2+1.178268607.025339102. // total potential energy u[i]=(u0[i]+u1[i]+u2[i]+u3[i]+u4[i])*convo.2)+pow(newzh2-min.709532773.0.025339102.2)+pow(newzh1-min.5).2)+pow(newyh2+1.375176933.203607710.6)). r14[i]=pow(pow(newxh1+0.0.2)+pow(newyh2-1.178268607.

j<=99. mindis=r[j]. v=min-incd. x1[2][1]=-sin(oorientation). } //calculating minimum energy after all possible rotaion along x-axis mminelement=minelement[0]. x1[2][0]=0. x1[1][1]=cos(oorientation). minangle=angle.i<=1400.cout<<"\t"<<"energy (in kJ/mol):"<<u[i]. } //storing minimum energy for a particular rotaion in an array minele=u[0]. oorientation=orientation[0]. //coordinate of H1. oorientation=orientation[i]. } } minelement[o]=minele. mmindistance=mindistance[0]. mmindistance=mindistance[i]. x1[0][1]=0.j++) { if(u[j]<minele) { minele=u[j]. mindis=r[0]. for(int i=0. x1[0][2]=0. min=v. mindistance[o]=mindis. orientation[o]=minangle.H3 and H4 31 .H2. } } //finding the coordinates of 5-site methane with minimum orientation position x1[0][0]=1. x1[1][2]=sin(oorientation). angle=minangle+inc.i++) { if(minelement[i]<mminelement) { mminelement=minelement[i]. for(int j=0. x1[2][2]=cos(oorientation). x1[1][0]=0.

txt"). fp. newzh4=newx4[0][2]+3. newxh2=newx2[0][0]. newxh3=newx3[0][0]. cout<<"\n"<<"\n"<<"and the coordinates of 5-site methane with minimum orientation position is : "<<"\n". newzh2=newx2[0][2]+3.k++) { newx1[j][k]=0.for(int j=0. cout<<"\n"<<"H3"<<"\t"<<newxh3<<"\t"<<newyh3<<"\t"<<newzh3. cout<<"\n"<<"H1"<<"\t"<<newxh1<<"\t"<<newyh1<<"\t"<<"\t"<<newzh1. newx2[j][k]=0. newx3[j][k]=newx3[j][k]+(x1[j][l]*h3[l][k]).l++) { newx1[j][k]=newx1[j][k]+(x1[j][l]*h1[l][k]).k<1.981339. newx3[j][k]=0.981339030. fp<<"\n"<<"H3"<<"\t"<<newxh3<<"\t"<<newyh3<<"\t"<<newzh3. newzh1=newx1[0][2]+3. 32 . newyh3=newx3[0][1].close().981339030. fp<<"\n"<<"H4"<<"\t"<<newxh4<<"\t"<<"\t"<<newyh4<<"\t"<<"\t"<<newzh4.981339030.141592654)<<" degree". fp."x. newyh1=newx1[0][1]. newx2[j][k]=newx2[j][k]+(x1[j][l]*h2[l][k]). newyh2=newx2[0][1].j<3. cout<<"\n"<<"\n"<<"\n"<<"Minimum energy well after all possible rotation along x-axis = "<<mminelement<<" kJ/mol". newx4[j][k]=0. newx4[j][k]=newx4[j][k]+(x1[j][l]*h4[l][k]). fp<<"\n"<<"H1"<<"\t"<<newxh1<<"\t"<<newyh1<<"\t"<<"\t"<<newzh1. cout<<"\n"<<"c0"<<"\t"<<0<<"\t"<<"\t"<<0<<"\t"<<"\t"<<3. cout<<"\n"<<"for an orientation of= "<<oorientation*(180/3. cout<<"\n"<<"at a distance of = "<<mmindistance<<" amgstrom". fp<<"\n"<<"c0"<<"\t"<<0<<"\t"<<"\t"<<0<<"\t"<<"\t"<<3. for(int l=0. newxh4=0. cout<<"\n"<<"H4"<<"\t"<<newxh4<<"\t"<<"\t"<<newyh4<<"\t"<<"\t"<<newzh4. cout<<"\n"<<"H2"<<"\t"<<newxh2<<"\t"<<newyh2<<"\t"<<newzh2.981339030.j++) { for(int k=0. fp<<"\n"<<"H2"<<"\t"<<newxh2<<"\t"<<newyh2<<"\t"<<newzh2. //storing the values of coordinates of methane with minimum energy ofstream fp.981339. } } } newxh1=newx1[0][0]. newzh3=newx3[0][2]+3.l<3.

h> #include<time. } 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<limits> 33 .return(0).

using namespace std.98133903-min.38*6.r24[100].085524733. incd=(mini-max)/100.mindis.u43[100].r26[100].inc.u3[100]. zh1=0.u25[100].r42[100].12)-pow(b/r0[i].0.mmindistance. float xh1. for(int i=0.6)).min.u35[100].newxh4.r0[100].minele.r46[100].891753667+pow(3.yh1.r31[100].r44[100].convo.xh4. u42[100].orientation[1400].r23[100].r12[100].5). float h1[3][1]. float r[100].newx3[3][1].r45[100].u26[100].u16[100].angle. convo=(1.yh3.newzh2.u0[100].r22[100]. u24[100].u11[100].yh4.u32[100].newxh3.h2[3][1].r15[100].b=3.u21[100].u4[100].022)/1000. 34 .zh4.newxh2.r13[100]. yh4=0.r32[100].mindistance[1400].r34[100].newzh3. minangle=0.v.u2[100].yh2.newx2[3][1].25602515.2.u36[100].r43[100]. int main() { float a=59.r25[100]. float r11[100].u23[100].u1[100].newyh4.d=3.u34[100]. cin>>mini>>[3][3].newx4[3][1].u14[100].u22[100].141592654).zh2. u0[i]=6*4*a*(pow(b/r0[i].u46[100].i<=99.max. newyh3.99995285.u12[100].06865175.o<=1400. u33[100].i++) { //interaction of C0 of methane with that of benzene r0[i]=pow(1.h3[3][1].o++) { min=mini. //coordinates of H4 with origin at centre of C-atom of methane xh4=0.u44[100].mminelement.h4[3][1].xh2. u15[100].zh3. yh1=-0.37689.718721927.r41[100].r35[100].r21[100].newzh1.r14[100].newzh4.r33[100].incd.u45[100].r36[100].2).u13[100].newxh1.r16[100].c=22.zh1. //conversion of unit of energy from K to kJ/mol //rotation of methane along y-axis about its c-atom for(int o=0.xh3. float minelement[1400]. using std::numeric_limits. xh1=-0. cout<<"Enter the min and max distance coordinate of benzene from methane ( if carbon of methane is at coordinate z=3.newyh2.newx1[3][1]. zh4=-1.newyh1.u41[100].u31[100]. oorientation. inc=(maxangle-minangle)/1440.maxangle=(2*3.98 and is above benzene): ".575.u[100].361841577. xh2=0.

025339102.275273359. newyh4=newx4[0][1]. newxh3=newx3[0][0]. h3[0][0]=xh3. x[2][2]=cos(minangle). x[2][1]=0. newyh1=newx1[0][1].361841577. newx2[j][k]=newx2[j][k]+(x[j][l]*h2[l][k]).yh2=-0.2)+pow(newzh4-min.l++) { newx4[j][k]=newx4[j][k]+(x[j][l]*h4[l][k]).2). newyh2=newx2[0][1]. for(int j=0. newxh2=newx2[0][0].5).2)+pow(newyh4+0. h2[1][0]=yh2. zh2=0. newyh3=newx3[0][1]. x[0][1]=0. newzh4=newx4[0][2]+3.0. newx2[j][k]=0.k++) { newx4[j][k]=0.178268607.732812593.0.j++) { for(int k=0. newx1[j][k]=0. h4[0][0]=xh4.5). for(int l=0. newx3[j][k]=0. h3[1][0]=yh3.981339030. h1[0][0]=xh1.0.375176933. h1[1][0]=yh1. xh3=0. 35 .361841577.5).988837743. x[1][0]=0.k<1. newzh2=newx2[0][2]+3.j<3.981339030. newx3[j][k]=newx3[j][k]+(x[j][l]*h3[l][k]). newx1[j][k]=newx1[j][k]+(x[j][l]*h1[l][k]).981339030. x[0][2]=-sin(minangle). h4[1][0]=yh4.203607710.2). r43[i]=pow(pow(newxh4-0. x[1][2]=0. h2[2][0]=zh2. newxh1=newx1[0][0].2).2)+pow(newyh4+1.2)+pow(newzh4-min.665644160. zh3=0. x[2][0]=sin(minangle).2)+pow(newyh4-1. yh3=0. r42[i]=pow(pow(newxh4-0. } } } newxh4=newx4[0][0]. newzh3=newx3[0][2]+3. x[0][0]=cos(minangle). h1[2][0]=zh1.2)+pow(newzh4-min. newzh1=newx1[0][2]+3.981339030. //interaction of H4 of methane with that of benzene r41[i]=pow(pow(newxh4-1. x[1][1]=1. h2[0][0]=xh2.709532773.l<3. h4[2][0]=zh4. h3[2][0]=zh3.

2).12)-pow(d/r45[i].2)+pow(newyh1-0.2).375176933.2)+pow(newyh1+1.5).6)).5).203607710. u32[i]=4*c*(pow(d/r32[i].12)-pow(d/r14[i]. u24[i]=4*c*(pow(d/r24[i].6)).375176933. r32[i]=pow(pow(newxh3-0.5). r33[i]=pow(pow(newxh3-0.2)+pow(newzh3-min. u4[i]=u41[i]+u42[i]+u43[i]+u44[i]+u45[i]+u46[i].665644160.665644160. //interaction of H3 of methane with that of benzene r31[i]=pow(pow(newxh3-1.0.665644160.2)+pow(newzh4-min.2).203607710.12)-pow(d/r41[i].12)-pow(d/r26[i]. r36[i]=pow(pow(newxh3+1.2). u34[i]=4*c*(pow(d/r34[i].0.178268607.2).2)+pow(newyh1+1.0.6)).178268607.2)+pow(newyh4-0. r46[i]=pow(pow(newxh4+1.6)).0.2)+pow(newyh1+0. u43[i]=4*c*(pow(d/r43[i]. u2[i]=u21[i]+u22[i]+u23[i]+u24[i]+u25[i]+u26[i].5).2)+pow(newzh2-min.2).12)-pow(d/r11[i].375176933.2)+pow(newzh2-min.0.2).709532773.0.2)+pow(newzh2-min.12)-pow(d/r16[i].203607710.5).709532773.5). r25[i]=pow(pow(newxh2+0.2)+pow(newzh3-min.2)+pow(newyh4-1.2)+pow(newyh3+1.665644160.12)-pow(d/r12[i].6)).709532773.2)+pow(newzh4-min.5).0. //interaction of H2 of methane with that of benzene r21[i]=pow(pow(newxh2-1.2)+pow(newzh2-min.12)-pow(d/r42[i]. r34[i]=pow(pow(newxh3+0.2)+pow(newyh2-1.0.665644160.5).6)). r45[i]=pow(pow(newxh4+0.12)-pow(d/r46[i].2)+pow(newyh3-1.2)+pow(newyh2-0.2)+pow(newzh1-min.6)).12)-pow(d/r22[i]. r14[i]=pow(pow(newxh1+0.178268607.0.12)-pow(d/r25[i]. r26[i]=pow(pow(newxh2+1.2)+pow(newzh3-min.2).2)+pow(newyh3-0.6)).6)).6)). 36 .203607710.12)-pow(d/r33[i]. u21[i]=4*c*(pow(d/r21[i]. u33[i]=4*c*(pow(d/r33[i].2)+pow(newzh3-min.5). r15[i]=pow(pow(newxh1+0.2)+pow(newzh2-min.6)).6)).2).2).2)+pow(newzh1-min. //interaction of H1 of methane with that of benzene r11[i]=pow(pow(newxh1-1.12)-pow(d/r31[i].203607710.178268607.2)+pow(newzh2-min. u31[i]=4*c*(pow(d/r31[i].12)-pow(d/r32[i]. u23[i]=4*c*(pow(d/r23[i].665644160.2). u16[i]=4*c*(pow(d/r16[i].0.6)).375176933.203607710.178268607.2)+pow(newyh1-1.r44[i]=pow(pow(newxh4+0. u45[i]=4*c*(pow(d/r45[i].2)+pow(newyh2+0.2)+pow(newzh3-min.2).5).6)).2)+pow(newzh1-min.5).025339102.2).5).2)+pow(newzh3-min. r13[i]=pow(pow(newxh1-0.2)+pow(newyh3+0.5).0.6)).2)+pow(newzh1-min.6)). u1[i]=u11[i]+u12[i]+u13[i]+u14[i]+u15[i]+u16[i].2).0.203607710.2).0.6)).12)-pow(d/r21[i].2)+pow(newzh1-min.2)+pow(newyh1-1. u26[i]=4*c*(pow(d/r26[i].12)-pow(d/r23[i].709532773. u46[i]=4*c*(pow(d/r46[i].2). u13[i]=4*c*(pow(d/r13[i].025339102.6)).2).12)-pow(d/r15[i].6)).178268607.709532773.709532773.0.12)-pow(d/r34[i].5).2). u12[i]=4*c*(pow(d/r12[i].025339102.375176933. u11[i]=4*c*(pow(d/r11[i]. r22[i]=pow(pow(newxh2-0.5).178268607.0. r23[i]=pow(pow(newxh2-0.2).0. u25[i]=4*c*(pow(d/r25[i].025339102. u15[i]=4*c*(pow(d/r15[i].6)). r16[i]=pow(pow(newxh1+1.375176933. r35[i]=pow(pow(newxh3+0.0.6)).025339102.2)+pow(newzh4-min.5).5).12)-pow(d/r43[i].025339102.12)-pow(d/r13[i]. u14[i]=4*c*(pow(d/r14[i].12)-pow(d/r24[i].0.025339102.665644160. r12[i]=pow(pow(newxh1-0.12)-pow(d/r44[i].709532773.2)+pow(newyh4+1.0.6)).0.2)+pow(newyh2-1.2). u22[i]=4*c*(pow(d/r22[i].0.5).5).2)+pow(newyh2+1.5). r24[i]=pow(pow(newxh2+0.2)+pow(newyh3+1.2)+pow(newyh3-1. u41[i]=4*c*(pow(d/r41[i].2)+pow(newzh1-min.2).375176933. u42[i]=4*c*(pow(d/r42[i].2)+pow(newyh2+1. u44[i]=4*c*(pow(d/r44[i].5).

u3[i]=u31[i]+u32[i]+u33[i]+u34[i]+u35[i]+u36[i]. u36[i]=4*c*(pow(d/r36[i]. angle=minangle+inc. minangle=angle. mindis=r[j].i<=1400.u35[i]=4*c*(pow(d/r35[i]. mmindistance=mindistance[0]. } //calculating minimum energy after all possible rotaion along y-axis mminelement=minelement[0]. // total potential energy u[i]=(u0[i]+u1[i]+u2[i]+u3[i]+u4[i])*convo. mmindistance=mindistance[i]. for(int i=0. mindis=r[0].6)). cout<<"\n"<<"distance (in amgstron) :"<<r[i].j<=99. r[i]=3.j++) { if(u[j]<minele) { minele=u[j]. orientation[o]=minangle.98133903-min. v=min-incd. for(int j=0. min=v. mindistance[o]=mindis.i++) { if(minelement[i]<mminelement) { mminelement=minelement[i]. oorientation=orientation[0].12)-pow(d/r35[i].12)-pow(d/r36[i]. 37 .6)). } } minelement[o]=minele. cout<<"\t"<<"energy (in kJ/mol):"<<u[i]. } //storing minimum energy for a particular rotaion in an array minele=u[0].

cout<<"\n"<<"\n"<<"\n"<<"Minimum energy well after all possible rotation along y-axis = "<<mminelement<<" kJ/mol". newx3[j][k]=newx3[j][k]+(x1[j][l]*h3[l][k]). newxh4=0. x1[1][0]=0. newx4[j][k]=0. newzh1=newx1[0][2]+3. newx2[j][k]=newx2[j][k]+(x1[j][l]*h2[l][k]). cout<<"\n"<<"H1"<<"\t"<<newxh1<<"\t"<<newyh1<<"\t"<<"\t"<<newzh1. 38 . } } //finding the coordinates of 5-site methane with minimum orientation position x1[0][0]=cos(minangle). newyh4=0.k++) { newx1[j][k]=0.l<3. cout<<"\n"<<"\n"<<"and the coordinates of 5-site methane with minimum orientation position is : "<<"\n".H2. newyh1=newx1[0][1]. newzh2=newx2[0][2]+3.j++) { for(int k=0.141592654)<<" degree". //coordinate of H1. newzh4=newx4[0][2]+3. newxh2=newx2[0][0].k<1.981339030. newzh3=newx3[0][2]+3. x1[0][1]=0. x1[2][1]=0. newx3[j][k]=0.981339.H3 and H4 for(int j=0.l++) { newx1[j][k]=newx1[j][k]+(x1[j][l]*h1[l][k]). } } } newxh1=newx1[0][0]. cout<<"\n"<<"c0"<<"\t"<<0<<"\t"<<"\t"<<0<<"\t"<<"\t"<<3. x1[1][1]=1. newyh2=newx2[0][1]. x1[2][2]=cos(minangle). x[2][0]=sin(minangle). x1[0][2]=-sin(minangle). newxh3=newx3[0][0]. cout<<"\n"<<"for an orientation of= "<<oorientation*(180/3.981339030. cout<<"\n"<<"at a distance of = "<<mmindistance<<" amgstrom". for(int l=0. cout<<"\n"<<"H2"<<"\t"<<newxh2<<"\t"<<newyh2<<"\t"<<newzh2.981339030. newx4[j][k]=newx4[j][k]+(x1[j][l]*h4[l][k]).j<3. x1[1][2]=0.oorientation=orientation[i]. newyh3=newx3[0][1]. newx2[j][k]=0.981339030.

fp.txt").open("y. fp<<"\n"<<"H4"<<"\t"<<newxh4<<"\t"<<"\t"<<newyh4<<"\t"<<"\t"<<newzh4.981339. cout<<"\n"<<"H4"<<"\t"<<newxh4<<"\t"<<"\t"<<newyh4<<"\t"<<"\t"<<newzh4. fp.close(). } program 5 : CALCULATING THE MINIMUM ENERGY WELL IN INTERACTION OF 5-SITE 39 . //storing the values of coordinates of methane with minimum energy ofstream fp. fp<<"\n"<<"c0"<<"\t"<<0<<"\t"<<"\t"<<0<<"\t"<<"\t"<<3. return(0). fp<<"\n"<<"H1"<<"\t"<<newxh1<<"\t"<<newyh1<<"\t"<<"\t"<<newzh1.cout<<"\n"<<"H3"<<"\t"<<newxh3<<"\t"<<newyh3<<"\t"<<newzh3. fp<<"\n"<<"H2"<<"\t"<<newxh2<<"\t"<<newyh2<<"\t"<<newzh2. fp<<"\n"<<"H3"<<"\t"<<newxh3<<"\t"<<newyh3<<"\t"<<newzh3.

yh4.98133903-min.r24[100].c=22.r45[100].u23[100].u25[100].u2[100]. zh1=0.minangle=3.r46[100].u[100]. 40 .newyh1.min.u14[100]. float h1[3][1].r44[100].x[3][3].convo.v. float minele.r35[100].r14[100].u13[100].i<=99.zh3.max.891753667+pow(3.r16[100].361841577.r43[100].u43[100].u34[100]. cout<<"enter the min and max distance of benzene from methane ( if carbon of methane is at coordinate z=3. //coordinates of H4 with origin at centre of C-atom of methane xh1=-0.0.newyh4.u45[100].5). u0[i]=6*4*a*(pow(b/r0[i].06865175.r36[100].newx2[3][1].mindis.newx3[3][1].h> #include<limits> using namespace std.newx1[3][1].u3[100]. cin>>min>>max.u36[100].h> #include<time.u41[100].newzh1.newxh4. u42[100].u26[100].newyh2.yh3.38*6.yh1. incd=(min-max)/100.r33[100]. newyh3.r0[100].2.r22[100]. int main() { float a=59. using std::numeric_limits.r42[100]. //conversion of unit of energy from K to kJ/mol // 180 deg ROTATION OF METHANE ALONG X-AXIS for(int i=0.yh2.newzh3. convo=(1.022)/1000.u22[100].r25[100].25602515.incd.d=3.u46[100].b=3.h4[3][1].u1[100].r13[100].u31[100].37689.newxh1.r34[100].xh3. float r11[100].zh2. float xh1.r41[100].r32[100].h2[3][1].zh4.98 and is above benzene: ".u12[100].METHANE (180 degree i.newxh3.zh1.6)).r23[100].u11[100].r26[100].u44[100].141592654. yh1=-0.xh4.99995285.u21[100].u0[100].575.newzh2. u15[100].i++) { //interaction of c0 with benzene r0[i]=pow(1.newzh4.newxh2.12)-pow(b/r0[i].2).r15[100].xh2.r31[100]. float r[100].u32[100]. u33[100].h3[3][1].u16[100]. u24[100].r21[100].r12[100].u4[100].u35[100].newx4[3][1].e. CH up) WITH BENZENE #include<iostream> #include<iomanip> #include<cstdio> #include<cmath> #include<fstream> #include<stdlib.

r45[i]=pow(pow(newxh4+0.732812593.k<1.2)+pow(newzh4-min.665644160.361841577.k++) { newx1[j][k]=0.2)+pow(newzh4-min. h3[0][0]=xh3. r43[i]=pow(pow(newxh4-0.0.2).j++) { for(int k=0. r46[i]=pow(pow(newxh4+1.j<3. newx3[j][k]=0.709532773.203607710.988837743. x[2][2]=cos(minangle). xh3=0.12)-pow(d/r42[i]. x[0][0]=1. newx2[j][k]=0.203607710. r41[i]=pow(pow(newxh4-1.361841577.718721927. x[0][2]=0. 41 .665644160.5).0.2)+pow(newyh4+1. r44[i]=pow(pow(newxh4+0. yh3=0.l++) { newx1[j][k]=newx1[j][k]+(x[j][l]*h1[l][k]).0.2)+pow(newzh4-min. newx3[j][k]=newx3[j][k]+(x[j][l]*h3[l][k]).2)+pow(newyh4-1.981339030. x[1][1]=cos(minangle). zh4=-1.12)-pow(d/r41[i].375176933.0. x[1][0]=0. x[0][1]=0.178268607.12)-pow(d/r43[i].0. h3[1][0]=yh3. newzh4=newx4[0][2]+3.2)+pow(newyh4-1.12)-pow(d/r46[i]. newx4[j][k]=newx4[j][k]+(x[j][l]*h4[l][k]).6)).2)+pow(newzh4-min. u44[i]=4*c*(pow(d/r44[i]. newyh4=newx4[0][1]. x[2][1]=-sin(minangle). h3[2][0]=zh3.6)).2)+pow(newyh4+0.2)+pow(newzh4-min.025339102.6)).2)+pow(newyh4+1. zh2=0.2).178268607. h4[2][0]=zh4. x[2][0]=0. h2[2][0]=zh2. h2[1][0]=yh2.6)).025339102.12)-pow(d/r44[i].6)).5).275273359. u41[i]=4*c*(pow(d/r41[i]. x[1][2]=sin(minangle).0. u45[i]=4*c*(pow(d/r45[i]. u42[i]=4*c*(pow(d/r42[i].2). h4[1][0]=yh4. yh4=0. xh4=0. newx4[j][k]=0. u46[i]=4*c*(pow(d/r46[i].2)+pow(newzh4-min. for(int j=0. h1[1][0]=yh1.2). newx2[j][k]=newx2[j][k]+(x[j][l]*h2[l][k]).2).6)).l<3.375176933.xh2=0. } } } //interaction of H4 with benzene newxh4=newx4[0][0]. h1[2][0]=zh1.5). r42[i]=pow(pow(newxh4-0. zh3=0.12)-pow(d/r45[i].5).5).709532773.5). h2[0][0]=xh2.2). h1[0][0]=xh1. h4[0][0]=xh4. for(int l=0.2)+pow(newyh4-0. u43[i]=4*c*(pow(d/r43[i].085524733. yh2=-0.

178268607. //interaction of H3 with benzene newxh3=newx3[0][0].178268607. //interaction of H1 with benzene newxh1=newx1[0][0].665644160. r24[i]=pow(pow(newxh2+0.5).2)+pow(newyh1+1.2)+pow(newzh1-min. u31[i]=4*c*(pow(d/r31[i]. r21[i]=pow(pow(newxh2-1.0.6)).2)+pow(newzh1-min.981339030.12)-pow(d/r24[i].375176933.2).0.12)-pow(d/r26[i].2)+pow(newzh2-min.178268607.2)+pow(newzh3-min.6)). u16[i]=4*c*(pow(d/r16[i].5).2). r13[i]=pow(pow(newxh1-0. u11[i]=4*c*(pow(d/r11[i].2)+pow(newzh1-min.2).12)-pow(d/r12[i].6)).2)+pow(newzh1-min. newyh1=newx1[0][1].0.2).375176933.6)).0.12)-pow(d/r31[i].2)+pow(newyh1+0. r23[i]=pow(pow(newxh2-0. r36[i]=pow(pow(newxh3+1.2)+pow(newzh3-min.2)+pow(newzh3-min.12)-pow(d/r13[i].0.5).5).2)+pow(newyh1-1.2)+pow(newyh3-1. u26[i]=4*c*(pow(d/r26[i].12)-pow(d/r21[i].2)+pow(newyh3+0.5).0.2)+pow(newyh2+0. r11[i]=pow(pow(newxh1-1.2).0.2).6)).2)+pow(newzh3-min. newzh1=newx1[0][2]+3.0.709532773.0.981339030. r14[i]=pow(pow(newxh1+0.2). u2[i]=u21[i]+u22[i]+u23[i]+u24[i]+u25[i]+u26[i].5).6)). u21[i]=4*c*(pow(d/r21[i]. r12[i]=pow(pow(newxh1-0.709532773.2)+pow(newzh3-min.375176933.6)).2).2)+pow(newyh1-0.2)+pow(newyh3-1.178268607.2).5). u13[i]=4*c*(pow(d/r13[i].375176933.0. newzh2=newx2[0][2]+3. newyh3=newx3[0][1].6)).2). r22[i]=pow(pow(newxh2-0.2)+pow(newzh2-min.0.2)+pow(newzh2-min. u24[i]=4*c*(pow(d/r24[i]. r33[i]=pow(pow(newxh3-0. u23[i]=4*c*(pow(d/r23[i].203607710.2)+pow(newzh3-min.0.665644160.u4[i]=u41[i]+u42[i]+u43[i]+u44[i]+u45[i]+u46[i].709532773.2)+pow(newyh1-1.2). r15[i]=pow(pow(newxh1+0.6)).665644160.025339102.203607710. r35[i]=pow(pow(newxh3+0.203607710. 42 .665644160.6)).2). u1[i]=u11[i]+u12[i]+u13[i]+u14[i]+u15[i]+u16[i].5).2)+pow(newyh3-0.2).203607710.178268607.2)+pow(newzh2-min.178268607.5).2)+pow(newyh2-0.12)-pow(d/r15[i]. //interaction of H2 with benzene newxh2=newx2[0][0]. u22[i]=4*c*(pow(d/r22[i].025339102. newyh2=newx2[0][1].203607710.2)+pow(newyh2-1.2).2). u12[i]=4*c*(pow(d/r12[i].6)).709532773.025339102.981339030.025339102.0.12)-pow(d/r11[i].025339102.0.709532773.5).0.6)).5).2). r31[i]=pow(pow(newxh3-1.2)+pow(newyh3+1.6)).12)-pow(d/r23[i].665644160.2)+pow(newyh3+1.12)-pow(d/r25[i]. u25[i]=4*c*(pow(d/r25[i].2)+pow(newzh2-min.5).0.5).2)+pow(newzh2-min. newzh3=newx3[0][2]+3. r25[i]=pow(pow(newxh2+0.12)-pow(d/r14[i]. r26[i]=pow(pow(newxh2+1.375176933. r34[i]=pow(pow(newxh3+0.025339102.2)+pow(newyh2-1. u14[i]=4*c*(pow(d/r14[i].2)+pow(newyh1+1.2)+pow(newyh2+1.5).12)-pow(d/r22[i].5).2)+pow(newzh1-min. r16[i]=pow(pow(newxh1+1.12)-pow(d/r16[i].2)+pow(newyh2+1.2).375176933.665644160.5).0. u15[i]=4*c*(pow(d/r15[i].5).2).5). r32[i]=pow(pow(newxh3-0.203607710.709532773.2)+pow(newzh1-min.0.

v=min-incd.6)). //finding the minimum energy well and corresponding distance for(int j=0.98133903-min.6)).12)-pow(d/r33[i]. min=v. mindis=r[0].t<=99. u36[i]=4*c*(pow(d/r36[i]. for(int t=0. } } cout<<"\n"<<"\n"<<"\n"<<"Minimum energy well for 0 deg(i. cout<<"\n"<<"distance (in amgstron) : "<<r[i].j<=99.close(). ofstream fp. u3[i]=u31[i]+u32[i]+u33[i]+u34[i]+u35[i]+u36[i].12)-pow(d/r32[i].u32[i]=4*c*(pow(d/r32[i]. cout<<"\n"<<"at a distance of = "<<mindis<<" amgstrom". u34[i]=4*c*(pow(d/r34[i].12)-pow(d/r35[i]. u33[i]=4*c*(pow(d/r33[i].j++) { if(u[j]<minele) { minele=u[j]. u35[i]=4*c*(pow(d/r35[i]. mindis=r[j].t++) { fp<<r[t]<<"\t"<<u[t]<<"\n".e.12)-pow(d/r34[i]. //storing the values of distance and energy in a file return(0).6)).txt"). fp. r[i]=3. cout<<"\t"<<"energy (in kJ/mol):"<<u[i].6)). // total potential energy due in rotation along x-axis u[i]=(u0[i]+u1[i]+u2[i]+u3[i]+u4[i])*convo. CH up) positon of methane = "<<minele<<" kJ/mol".6)). } 43 . } minele=u[0].12)-pow(d/r36[i].open("r. } fp.

convo. using std::numeric_limits. //conversion of unit of energy from K to kJ/mol // ROTATION OF METHANE ALONG Z-AXIS BY 5 degrees for(int o=0.h3[3][1].newx3[3][1].r31[100].98 and is above benzene: ".r25[100].u[100].u23[100].min. cin>>mini>>max.newxh1.r44[100].575.h4[3][1].r34[100].r45[100].x[3][3]. newyh3.r41[100].newzh2.r26[100].zh3.u35[100]. u33[100].r13[100]. u42[100].r33[100].u14[100]. incd=(mini-max)/[100].maxo.xh4.mminelement. float h1[3][1]. float xh1. float r11[100]. float minelement[1400].141592654).xh2.u44[100].b=3.u3[100].xh3.r35[100].yh4.38*6. int main() { float a=59.u13[100].newx1[3][1].maxd.u12[100].newyh4.2.u26[100].newyh1.r43[100].zh2.u43[100].angle.u25[100].r42[100].maxe.c=22.u22[100].r14[100].u2[100].37689.max. u15[100]. newx4[3][1]. inc=(maxangle-minangle)/72.u1[100]. u24[100].h> #include<limits> using namespace std.r22[100].mindis.r15[100].u36[100].r46[100].o<=72.newyh2.r32[100]. orientation[1400].newxh4.zh4.v.r36[100].zh1.r21[100].newzh3.h> #include<time. cout<<"enter the min and max distance of benzene from methane ( if carbon of methane is at coordinate z=3.u11[100].u21[100].u32[100][100].r0[100].incd.06865175.u34[100].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. maxangle=(2*3. convo=(1.newzh4.h2[3][1].yh2.r23[100].r16[100].d=3.oorientation. float r[100].u0[100].u46[100].newx2[3][1].022)/1000.mmindistance.minangle=0.r24[100].u45[100].u16[100].o++) { 44 .u31[100].newxh2.minele.yh1.u4[100].mindistance[1400].yh3.x1[3][3].

x[1][0]=-sin(minangle). h3[2][0]=zh3. x[2][0]=0.988837743. newyh4=newx4[0][1]. for(int i=0. newx3[j][k]=newx3[j][k]+(x[j][l]*h3[l][k]).0. x[1][1]=cos(minangle). newx2[j][k]=0. newx4[j][k]=0. x[2][2]=1. xh2=0. h4[1][0]=yh4. for(int l=0. zh3=-0.i<=99. newx2[j][k]=newx2[j][k]+(x[j][l]*h2[l][k]). h4[0][0]=xh4.12)-pow(b/r0[i].275273359.361841577. h1[2][0]=zh1.98133903-min. newx3[j][k]=0. h3[1][0]=yh3.k++) { newx1[j][k]=0. xh1=-0.361841577.25602515.718721927. newx4[j][k]=newx4[j][k]+(x[j][l]*h4[l][k]). zh1=-0. h3[0][0]=xh3. h2[1][0]=yh2.085524733.99995285.l++) { newx1[j][k]=newx1[j][k]+(x[j][l]*h1[l][k]). yh1=0. yh3=-0. h4[2][0]=zh4.5). x[1][2]=0. h1[0][0]=xh1. } } } //interaction of H4 with benzene newxh4=newx4[0][0]. for(int j=0.j<3. zh2=-0.361841577.j++) { for(int k=0. h1[1][0]=yh1.l<3.2). //coordinates of H4 with origin at centre of C-atom of methane xh4=0.k<1. h2[2][0]=zh2. yh2=0.891753667+pow(3. x[2][1]=0. yh4=0. h2[0][0]=xh2. u0[i]=6*4*a*(pow(b/r0[i]. 45 . x[0][1]=sin(minangle). zh4=1.6)).min=mini. xh3=0.732812593. x[0][2]=0.i++) { //interaction of c0 with benzene r0[i]=pow(1. x[0][0]=cos(minangle).

2).2)+pow(newyh2+1.0.12)-pow(d/r45[i].12)-pow(d/r44[i]. 46 .12)-pow(d/r26[i].2)+pow(newyh1-0.2)+pow(newyh2-0.375176933.2)+pow(newyh2-1.2). r41[i]=pow(pow(newxh4-1.6)).2).2). u1[i]=u11[i]+u12[i]+u13[i]+u14[i]+u15[i]+u16[i].178268607. u26[i]=4*c*(pow(d/r26[i].2).025339102.2)+pow(newyh4+1. newzh1=newx1[0][2]+3.665644160.6)).665644160.665644160.2)+pow(newzh2-min.203607710.2). u44[i]=4*c*(pow(d/r44[i].5).5).12)-pow(d/r12[i].203607710. r46[i]=pow(pow(newxh4+1.12)-pow(d/r24[i].203607710.203607710.2)+pow(newyh2+0.5).2)+pow(newyh2+1.5).5). r21[i]=pow(pow(newxh2-1.12)-pow(d/r15[i].12)-pow(d/r43[i]. u14[i]=4*c*(pow(d/r14[i]. newyh2=newx2[0][1].2).2)+pow(newzh1-min.2)+pow(newzh4-min.2)+pow(newyh1+1. u16[i]=4*c*(pow(d/r16[i].12)-pow(d/r22[i]. r24[i]=pow(pow(newxh2+0. newyh1=newx1[0][1].0. u15[i]=4*c*(pow(d/r15[i].5).2).0.2).6)). u24[i]=4*c*(pow(d/r24[i].2).025339102.2). u13[i]=4*c*(pow(d/r13[i].5). r42[i]=pow(pow(newxh4-0.0. u21[i]=4*c*(pow(d/r21[i].6)).981339030.12)-pow(d/r14[i].6)).6)). //interaction of H1 with benzene newxh1=newx1[0][0]. u25[i]=4*c*(pow(d/r25[i].5). u11[i]=4*c*(pow(d/r11[i].5).709532773.0.025339102.6)).12)-pow(d/r41[i].0.025339102. r44[i]=pow(pow(newxh4+0.375176933.0. r26[i]=pow(pow(newxh2+1.0.6)).12)-pow(d/r11[i].0.981339030.2)+pow(newyh4-1.2)+pow(newyh4-1.0. u42[i]=4*c*(pow(d/r42[i].6)).665644160. u4[i]=u41[i]+u42[i]+u43[i]+u44[i]+u45[i]+u46[i].12)-pow(d/r13[i].025339102.375176933.203607710.0.709532773.0.178268607.2)+pow(newzh4-min.2)+pow(newyh1+1. r12[i]=pow(pow(newxh1-0.709532773. u46[i]=4*c*(pow(d/r46[i].203607710.6)).2)+pow(newzh4-min.709532773.2)+pow(newyh1-1.178268607.2).2)+pow(newzh2-min.2)+pow(newyh1+0.178268607. //interaction of H2 with benzene newxh2=newx2[0][0].2).2)+pow(newyh4+1.6)).2)+pow(newyh4-0.0.2)+pow(newzh1-min.0.2). u22[i]=4*c*(pow(d/r22[i].375176933.665644160.2)+pow(newyh4+0.178268607.5).2)+pow(newyh1-1. r22[i]=pow(pow(newxh2-0.2).375176933.6)).665644160.5).5).178268607.2)+pow(newzh1-min. r13[i]=pow(pow(newxh1-0.2)+pow(newzh1-min.2)+pow(newzh4-min.2)+pow(newzh2-min.5). r15[i]=pow(pow(newxh1+0.2)+pow(newzh1-min.newzh4=newx4[0][2]+3.2)+pow(newzh1-min.5).709532773.2)+pow(newzh2-min. r23[i]=pow(pow(newxh2-0.2)+pow(newzh2-min.0.12)-pow(d/r46[i].12)-pow(d/r42[i].6)).12)-pow(d/r21[i]. r43[i]=pow(pow(newxh4-0. r45[i]=pow(pow(newxh4+0. u41[i]=4*c*(pow(d/r41[i].709532773. r25[i]=pow(pow(newxh2+0.0.2).6)).6)).12)-pow(d/r23[i].12)-pow(d/r16[i].5).2)+pow(newzh2-min. newzh2=newx2[0][2]+3.12)-pow(d/r25[i].0.981339030.5).375176933. u43[i]=4*c*(pow(d/r43[i].025339102.6)). r14[i]=pow(pow(newxh1+0.2)+pow(newyh2-1.6)).5). r16[i]=pow(pow(newxh1+1.2).0.6)). u23[i]=4*c*(pow(d/r23[i].2). u45[i]=4*c*(pow(d/r45[i]. u12[i]=4*c*(pow(d/r12[i].5). r11[i]=pow(pow(newxh1-1.2)+pow(newzh4-min.2)+pow(newzh4-min.

fp.2)+pow(newzh3-min.665644160.2).375176933.12)-pow(d/r36[i].2).178268607.6)).203607710.0.709532773. min=v. for(int j=0.2)+pow(newyh3-1. orientation[o]=minangle.5).2)+pow(newzh3-min.6)). v=min-incd.5).t<=72.2)+pow("z. r35[i]=pow(pow(newxh3+0.0. u35[i]=4*c*(pow(d/r35[i].6)).j++) { if(u[j]<minele) { minele=u[j]. //interaction of H3 with benzene newxh3=newx3[0][0].2)+pow(newzh3-min.2)+pow(newzh3-min. mindistance[o]=mindis.025339102.025339102.2). mindis=r[0].12)-pow(d/r34[i].2)+pow(newyh3-1.98133903-min.12)-pow(d/r33[i].12)-pow(d/r32[i]. r34[i]=pow(pow(newxh3+0.981339030.2)+pow(newyh3+1. u36[i]=4*c*(pow(d/r36[i].5).2).5).2).178268607. r31[i]=pow(pow(newxh3-1.2)+pow(newyh3+0.0. u34[i]=4*c*(pow(d/r34[i]. u32[i]=4*c*(pow(d/r32[i]. r32[i]=pow(pow(newxh3-0.5). r[i]=3.375176933. mindis=r[j].j<=99. u33[i]=4*c*(pow(d/r33[i].709532773. u31[i]=4*c*(pow(d/r31[i].2)+pow(newzh3-min.6)).u2[i]=u21[i]+u22[i]+u23[i]+u24[i]+u25[i]+u26[i]. r33[i]=pow(pow(newxh3-0. } //minimum energy for a particular rotaion minele=u[0]. newyh3=newx3[0][1].12)-pow(d/r31[i].5). newzh3=newx3[0][2]+3.12)-pow(d/r35[i]. u3[i]=u31[i]+u32[i]+u33[i]+u34[i]+u35[i]+u36[i].2)+pow(newyh3+1.665644160.2).txt").6)). } } minelement[o]=minele. //storing the variaation of energy with angle of rotation along z-axis ofstream fp. // total potential energy due in rotation along x-axis u[i]=(u0[i]+u1[i]+u2[i]+u3[i]+u4[i])*convo.2)+pow(newzh3-min. for(int t= { 47 .203607710. r36[i]=pow(pow(newxh3+1.

141592654)<<"\t"<<minelement[t]<<"\n". //minimum energy after all possible rotaion along z-axis for(int i=0. x1[2][1]=0. x1[0][1]=sin(oorientation). x1[0][2]=0. x1[1][1]=cos(oorientation). 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). angle=minangle+inc. } } 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".fp<<orientation[t]*(180/3.i++) { if(minelement[i]<mminelement) { mminelement=minelement[i]. maxd=mindistance[0]. maxo=orientation[0]. x1[1][0]=-sin(oorientation).141592654)<<" degree". mmindistance=mindistance[0].141592654)<<" degree". x1[2][0]=0. maxo=orientation[j]. maxe=minelement[0]. x1[2][2]=1.i<=72. minangle=angle. } } cout<<"\n"<<"\n"<<"\n"<<"Maximum energy well after all possible rotation along z-axis = "<<maxe<<" kJ/mol". oorientation=orientation[i].j++) { if(minelement[j]>maxe) { maxe=minelement[j]. cout<<"\n"<<"at a distance of = "<<maxd<<" amgstrom".close(). oorientation=orientation[0]. 48 .j<=72. } mminelement=minelement[0]. cout<<"\n"<<"for an orientation of= "<<oorientation*(180/3. cout<<"\n"<<"for an orientation of= "<<maxo*(180/3. } fp. mmindistance=mindistance[i]. x1[1][2]=0. //maximum energy well among all ipossible rotaion along z-axis for(int j=0. maxd=mindistance[j].

981339030.981339030. newxh4=0.l<3.H3 and H4 for(int j=0.txt"). newzh1=newx1[0][2]+3. fp<<"\n"<<"H2"<<"\t"<<newxh2<<"\t"<<newyh2<<"\t"<<newzh2. newyh4=0. fp. newzh4=newx4[0][2]+3.//coordinate of H1.k++) { newx1[j][k]=0.close(). newxh3=newx3[0][0].981339030. fp<<"\n"<<"c0"<<"\t"<<0<<"\t"<<"\t"<<0<<"\t"<<"\t"<<3. fp. cout<<"\n"<<"H4"<<"\t"<<newxh4<<"\t"<<"\t"<<newyh4<<"\t"<<"\t"<<newzh4.981339.j<3. newxh2=newx2[0][0].j++) { for(int k=0. fp<<"\n"<<"H1"<<"\t"<<newxh1<<"\t"<<newyh1<<"\t"<<newzh1. 49 . cout<<"\n"<<"c0"<<"\t"<<0<<"\t"<<"\t"<<0<<"\t"<<"\t"<<3. fp<<"\n"<<"H4"<<"\t"<<newxh4<<"\t"<<"\t"<<newyh4<<"\t"<<"\t"<<newzh4. for(int l=0. cout<<"\n"<<"H2"<<"\t"<<newxh2<<"\t"<<newyh2<<"\t"<<"z1. newx3[j][k]=newx3[j][k]+(x1[j][l]*h3[l][k]). cout<<"\n"<<"H3"<<"\t"<<newxh3<<"\t"<<newyh3<<"\t"<<newzh3. newx4[j][k]=0.981339030. newyh2=newx2[0][1]. newx2[j][k]=0. newzh3=newx3[0][2]+3. newyh3=newx3[0][1].l++) { newx1[j][k]=newx1[j][k]+(x1[j][l]*h1[l][k]). cout<<"\n"<<"H1"<<"\t"<<newxh1<<"\t"<<newyh1<<"\t"<<newzh1. fp<<"\n"<<"H3"<<"\t"<<newxh3<<"\t"<<newyh3<<"\t"<<newzh3. //storing the values of coordinates of methane with minimum energy ofstream fp. newyh1=newx1[0][1]. cout<<"\n"<<"\n"<<"The coordinates of 5-site methane with minimum energy orientation position(i.981339. newx3[j][k]=0.e. newzh2=newx2[0][2]+3. newx2[j][k]=newx2[j][k]+(x1[j][l]*h2[l][k]).k<1. newx4[j][k]=newx4[j][k]+(x1[j][l]*h4[l][k]).H2. after rotation by 15 degrees) is : "<<"\n". } } } newxh1=newx1[0][0].

S.  Chingombe.. and Sherrill. (2006) Aliphatic CH/π interactions: Methane-benzene. M.  Ashley.. F. C. Saha. Rood Department of Civil Engineering. } References  Vinay’s thesis.. L. Jian Sun. 553–566.return(0). Urbana. D. first edition. France.  Allen_M. Dr. Figgs. Alain Celzard_Professor at the University Henri Poincaré of Nancy._Computer_simulation_of_liquids_(1987). Some procedures with reduced errors._J. 3132–3143. 50 . Carbon 43(15)._P. University of Illinois 205 rth Mathews Ave. methane-phenol. (2006) Global Warming: Understanding the Forecast. IL 61801  Methane storage: Adsorption fundamentals and preparation of an ideal carbonaceous adsorbent.. Sinnokrot. P. and methane-indole complexes. Brady and Mark J. M. Role of functional groups on adsorption of methane and carbon dioxide in activated carbons (2011). Wiley-Blackwell._Tildesley_D.  Boys. and Bernardi. R. Molecular Physics 19(4). (2005) Surface modification and characterisation of a coal-based activated carbon.. and Wakeman. B.  ADSORBED NATURAL GAS STORAGE WITH ACTIVATED CARBON. Todd A. (1970) The calculation of small molecular interactions by the differences of separate total energies.  Archer.

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