Lab
Report on Molecular Modeling
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Lab Report on Molecular Modeling
Table of contents
Topic
1. Purpose…………………………………………………….3
2. Introduction………………………………………………..3
3. Procedure
and observation………………………………...3-10
4. Discussion
and conclusion………………………………..10-11
5. References………………………………………………...12
Purpose
The molecular
modeling provides a descriptive analysis of how the Spartan program is used in
molecular modeling and naming of organic compounds and molecules using their 3D
structures and by calculating the energy formation of the organic structures (Juanes
et al., 2017). The computer program will, therefore, create and analyze 3D
structures of the organic compounds showing the outline of their constituent
molecules and their bond angles. The experiment was therefore done to advance
the understanding of the 3D molecular shapes of structures.
Introduction
Organic compounds
and structures have varied molecular structures with different isomerism
depending on the constituent elements and the bonding structures involved. The
Spartan computer program is used to build their 3D structures and, as a result,
calculate the bond energies involved. This lab report can be grouped into two
sections. The sections are the identification of the molecular energies and the
isomerism of cyclohexene.
Procedure
and Observation
1.
Identification of molecular energies
Molecular energies of various organic compounds differ
depending on several factors, such as; the types of bonds involved, the bond
angles, and the number of carbon atoms present in the given molecule (Seonah, Fioroni, & al, 2019). Derivation
of the stated concept requires that one understand the following:
i.
The building and finding of conformation
energies for Butane and the disubstituted Ethane
The
process involved the drawing of Butane using the Spartan program. Through the
Setup menu, the molecular mechanics were used to calculate equilibrium geometry
for each molecule in the structure of Butane. The structure of Butane was set,
as seen in the diagram (a) below.
Diagram
(a): Butane
From
the structure, Butane indicated energy of -21.2379KJ/mol
ii.
Identification of alternative
conformations of molecules
Then, the structure was
adjusted to attain a dihedral angle of 00, thus generating energy of
5593KJ/mol, which was much higher than the initial structure. The figure below
is a representation of the dihedral structure of Butane at 00.
Diagram
(b): Butane with a dihedral angle 00.
Through
continuous adjustments of the dihedral angles of butane, the adjustments at 600
, 1200 , 1800 , 2400 , 3000 ,
and 3600 resulted to -17.7217KJ/mol, -17.9651KJ/mol, -21.2379KJ/mol,
-4.6788KJ/mol, -17.9651KJ/mol and 0.5593KJ/mol respectively. The diagrams below
illustrate the information obtained from the Spartan program at various angles
of adjustment of the dihedral butane molecule.
Diagram (c) N- Butane Dihedral 120-degree Diagram (d) N- Butane Dihedral
180 degree
Energy: -17.9651 kJ/mol
Energy: -21.2379 kJ/mol
Diagram (e) N- Butane Dihedral 240-degree Diagram (f) N- Butane Dihedral
300 degree
Energy: -4.6788 kJ/mol Energy:
-17.9651 kJ/mol
Diagram (g) N- Butane Dihedral 360 degree
Energy: 0.5593 kJ/mol
a. The
determination of conformation energies for disubstituted Ethane or Propyl
halide
Using the compound
structures of 1-bromo-2-fluoro-ethane at various degrees of adjustments, with
the constant two carbon atoms, the positions of the halides conformed to the
energies obtained through the substitution process.
The alteration of
the position of the halides, at angles of 00,600, 1200,
1800, 2400, 3000, and 3600 resulted
in the formation of the 1-bromo-2-fluoro-ethane as shown in the diagrams below;
0 degree
60 degree
52.9763 kJ/mol 23.3104 kJ/mol
120 degree 180 degree
33.1564 kJ/mol 21.9698 kJ/mol
240 degree 300 degree
360.1564
KJ/mol
23.3104 kJ/mol
360 degree 23.3104 KJ/mol
b. Identification
of the molecular energies for various organic compounds and the isomerism of
cyclohexene
This
section involved the drawing and naming of some molecular structures of
cyclohexane with different bond energies. The molecular structures were named
as below;
Discussion
and Conclusion
According to the
various levels of transition at various angles of the molecules, the
conformation of the structures changes forming either axial or equatorial
structures (Phiena, Liubov, Ágúst, & al,
2018). The equatorial structures resulted from the existence of the six
peripheral hydrogen atoms attached to the carbon ring forming the cyclohexane
while the axial structure resulted when similarly six hydrogen atoms are
arranged parallel to the symmetrical alignment of the cyclohexane ring (Dietmar, Farmer, & Matthews, 2019). In
relation to the various structures, the equatorial structures are more stable
compared to the axial. The axial structures have their carbon to carbon bonds
larger compared to the carbon to hydrogen, thus increasing their steric
crowding compared to the closely packed equatorial structures (CarloS, Nieto, Frank, & Kolocouris, 2016).
The Spartan
program provided a three-dimensional display of the various structures of the
molecular compounds by building the exact models of the molecules. The program
was, therefore, useful in obtaining a visual shape of the various molecules and
providing the energy calculation for the various sophisticated compound
molecules. The molecular spectra of each of the molecules.
References
CarloS,
L., Nieto, F., Frank, D., & Kolocouris, F. (2016). Assessing the
attractive/repulsive force balance in axial cyclohexane C–Hax···Yax contacts—a
combined computational analysis in monosubstituted cyclohexanes, Retrieved
from https://onlinelibrary.wiley.com/doi/abs/10.1002/jcc.24496.
Dietmar,
K., Farmer, S., & Matthews, K. (2019). Axial and Equatorial Bonds in
Cyclohexane. Cyclohexane Conformations, Retrieved from:
https://chem.libretexts.org/Bookshelves/Organic_Chemistry/Map%3A_Organic_Chemistry_(McMurry)/04%3A_Organic_Compounds-_Cycloalkanes_and_their_Stereochemistry/4.07%3A_Axial_and_Equatorial_Bonds_in_Cyclohexane.
Seonah,
K., Fioroni, M., David J.Robichaud, Dhrubajyoti D., Das and Peter C. St.John
(2019). Experimental and theoretical insight into the soot tendencies of the
methyl cyclohexene isomers. Proceedings of the Combustion Institute,
Volume 37, Issue 1, 2019, Pages 1083-1090. Retrieved from:
https://www.sciencedirect.com/science/article/pii/S1540748918302785.
Tran
Dinh Phiena, Liubov E.Kuzmina, Ágúst Kvaran, Sigridur Jonsdottir, Ingvar
Arnason, Sergey A.Shlykov (2018). Cyanocyclohexane. Axial-to-equatorial
“seesaw” parity in gas and condensed phases, Retrieved from
https://www.sciencedirect.com/science/article/abs/pii/S0022286018305696.
