The Theoretical Basic
Molecular Mechanics or force-field methods use classical type models to predict the energy of a molecule as a function of its conformation. This allows predictions of
•Equilibrium geometries and transition states
•Relative energies between conformers or between different
Molecules Molecular mechanics can be used to supply the potential energy for molecular dynamics computations on large molecules.
Conformation is configuration and compilation of structure of molecules. The conformation of a molecule containing two tetrahedral atoms linked together can be represented as a "sawhorse" or as a Newman projection. In the Newman projection the molecule is viewed along the axis of a rotatable bond.
COMPASS (some types of COMPASS: MM3, CHARMM, AMBER, and CFF) stands for Condensed-phase Optimized Molecular Potentials for Atomistic Simulation Studies. COMPASS represents the state-of-the-art forcefield technology. It is the first ab initio forcefield that enables accurate and simultaneous prediction of structural, conformational, vibrational, and thermophysical properties for a broad range of molecules in isolation and in condensed phases. Same with CFF forcefield, PCFF is an ab initio forcefield. Most parameters are derived from ab initio data using a least-squares fitting technique developed by Hagler and coworkers [2].
The number of such conformations (conformers) depends on the number of energy minima on the energy profile. In the case of ethane molecule three energy minima are encountered during 360o rotation. These minima correspond to "staggered" conformers. Unless it is specifically justified by certain constraints, most conformations of acyclic compounds are staggered. The maxima on the energy potential correspond to "eclipsed" conformations.
Molecular mechanics can be illustrated by the total energy as a sum of Taylor series expansions for stretches for chain of atoms. To illustrate the potential energy depends on some energy following the equation (1).
Molecular Dynamics depends on a temperature in the system, further analysis for conformations, thermodynamic properties and dynamic behavior of molecules [3].
Experimental
In this experiment we have to simulate butane, polyethylene, 20 repeat units of ethane and 20 repeat unit of ethane with sulphur atom in center of chains by Materials Studio 4.2 software.
In the first section of this simulation we sketched and analyzed the butane structure. Thus perform molecular mechanics by setting the angles and distances of atoms and minimization (the setup tool was used to set the force field: pcff, which is ideal for small carbon based molecules)by changing the angle from -180o to 180o with interval 30o the butane structure to get properties of butane structure in the initial and final values.
The second step we have to simulate dynamic simulation of butane at 500 K and 200 K for 1000 ps. The image will be imaged every 100 fs. In this section we got history of dihedral distribution by effect of temperature.
In the second project of this experiment we have to analyze Polyethylene with 30 repeating unit. in this section we was using dynamic simulation at 500 K for 100 ps and for 600 ps to know end to end distance in result image. In the end we have to calculate Kuhn Segment by equation 2>=L I.
In the third project we have to create poly ethylene with 20 repeat units and set the pcff force and minimization (same to do with the first project). In this section we vet to compare between the pure structure of 20 repeat unit ethylene and the center one of sulphur in the 20 repeat unit structures.
In this simulation of butane we have result of before and after value of minimization in table 1. We can analyze that total potential energy can be influenced by torsion angle. In this simulation we can get the lowest value at 0o of range from -180o to 180o that it is same with theory of conformation about "staggered" conformation.
Table1.The value of minimization potential energy of butane
Initial Minimization
Final Minimization
Total potential energy
Angle
Potential Energy
Angle
Potential Energy
-180
2.933969
-179.984
-5.52051
-8.45448
-150
-3.77079
-179.983
-5.52051
-1.74973
-120
-1.96814
-179.981
-5.52051
-3.55237
-90
-3.46241
-65.6441
-4.62296
-1.16056
-60
4.812918
-65.5942
-4.62296
-9.43588
-30
1.415253
-65.6455
-4.62296
-6.03822
0
16.36498
-65.595
-4.62296
-20.9879
30
1.415253
65.5913
-4.62296
-6.03822
60
3.72776
65.5921
-4.62296
-8.35072
90
5.375054
65.6405
-4.62296
-9.99802
120
7.149971
65.645
-4.62296
-11.7729
150
4.895981
179.984
-5.52051
-10.4165
180
2.933969
179.984
-5.52051
-8.45448
Correlated to table 1 we can see the graphics of these values in figure2
In the second part of dynamics simulation of butane, we can know dihedral distribution in the difference temperature (200 K and 500 K) (we can see detail figure3 and figure4). We can analyze that the stability of molecular at 500 K higher than 200 K. We can say that temperature can effect in mobility of molecular. On the other analysis we can predict that the stable configuration occurs at low temperature.
In the second project of polyethylene with 30 repeat units, we also simulate the dynamics molecular (long
chains) for knowing mobility of molecular the stretched molecule, the longer the period for which the chain is simulated. We can see in figure5 and figure6 that the distribution of distance for 600 ps can be reached higher than for 100 ps. We can get the distribution of distance completely coil for longer time.
We can see that result of End to end distance 2>, and Kuhn Segment (ℓ) in table 2 by equation “[1]. Before calculation the values we can know the value of contour length by normal condition. 2> can be obtained by calculating simulation data of end to end distance function of the time.
Table2. The Values of Kuhn segment length parameters of poly ethylene for 100 ps and 600 ps
Parameters
100 ps
600 ps
End to end distance 2> [Å2]
3630.424
1726.90
Kuhn Segment (ℓ), [Å]
48.0132
22.839
Contour Length (L) [Å]
75.613
75.613
In the final project we have to compare the structure of a minimized homogeneous polyethylene chain and aminimized polyethylene chain with sulphur in the center of structure. We can see it detail in the figure7 which there is difference of structure because how many of hand of sulphur can link hydrogen chain.
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