Molecular Modeling with Spartan

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 0^0, 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.