Introduction to Molecular Modeling & Independent Molecular Modeling Project. Certain properties and characteristics of different molecules were observed via molecular modeling using the computer software PC Spartan Pro. Specifically, two molecules were se

Figure 2: Electron Density of Azomethine Ylide

        Figure 2 shows the distribution of electrons in azomethine ylide. By convention, red areas represent electron-rich regions while blue areas are those for electron-poor egions. The figure shows that nitrogen, being a highly electronegative compound, causes electrons to spend most of the time near the said atom. Away from N, the other regions of the molecule become more electron poor. This implies that the electrons of azomethine ylide are attracted to the electronegative N. Because of this, azomethine ylide has a dipole moment pointing upward (1.578 D).

For the second model, indole, single-point energy with Hartee-Fock 3-21G calculations using AM1 semi-empirical equilibrium geometry was employed. The AM1 semi-empirical module was used to enable the calculations to be based on the lowest-energy conformer of the molecule. Figure 1 below presents the computer-generated model of indole.

Figure 3: PC Spartan Pro-Generated Structure of Indole

        Figure 3 depicts the organic molecule indole as a bicyclic structure consisting of a six-membered benzene ring fused to a five-membered N-containing pyrole ring. The AM1 geometry bond distances in the pyrole ring were investigated by obtaining the bond lengths of the C-C and C-N bonds of indole (in terms of Angstroms). Table 1 below presents the said values:

Table 1: C-C and C-N Bond Lengths of Indole

        Table 1 shows that the values of C-C and C-N bond length do not deviate from each other significantly (ranging from 1.370 to 1.422 Å). The last four values are that of the bonds in the pyrole ring. For the C8-N, N-C1 and C1-C2 bonds, the lengths are at a comparable range of 1.370 to 1.377 Å, while the C7-C1 only deviated a bit from the other three (1.422 Å). This close range of values implies that the bond lengths in the pyrole ring are relatively similar and that bonding in indole is delocalized. Otherwise, C-C and C-N double bonds are expected to be shorter than C-C and C-N single bonds. The relatively similar bond lengths of indole indicate that bonds are delocalized and that the molecule has a planar geometry. Moreover, counting the number of electrons in the delocalized p-orbital cloud reveals that there are 10 π-electrons, following the 4n+2 rule (Huckel rule) for the aromaticity of compounds, which in this case, n=2. All of these verify the aromaticity of indole, since aromatic compounds are known for their delocalized π-electrons, and this delocalization results to planar geometry.

Conclusion:

        Molecular modeling was employed in this activity to examine specific characteristics of azomethine ylide and indole. For azomethine ylide, electron density was calculated to examine the molecule’s observed dipole. By electron density mapping, it was figured out that the electronegative N atom tends to attract electrons of the molecule to it, which in turn causes the observed dipole. For indole, the relatively similar bond lengths imply that the said molecule has a delocalized charge and planar geometry. In both its benzene and pyrole rings, the π-electrons are delocalized.

References:

http://www.usm.maine.edu/~newton/Chy251_253/Lectures/Aromaticity/AromaticityFS.html. <date accessed: Feb. 20, 2011>

http://www.chem.ucalgary.ca/courses/351/Carey5th/Ch11/ch11-3.html. <date accessed: Feb. 20, 2011>

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