Moleular Modelling

Published: 2021-09-14 20:05:09
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Bob Lee September 24, 2012
Hong Zhao Section 248
Introduction to Molecular Modeling
When representing molecules, a 2D-perspecitve is not sufficient enough to understand the chemical properties associated with the molecule. With a 3-D perspective molecule, we can see the position of each molecule in space with the assistance of the extra dimension. This means that we can see which molecules actually exist behind the plane, in the plane, and ones pointing out of the plane. For this experiment, the 3D model was used to portray the molecule with different bond angles. Differing bond angles provided the molecule with varying energies due to the position of the bonded groups. From the 3-D view, a newman projection was able to be made. This projection usually is specific to two carbons and how the attached groups are oriented with respect to each other.

The orientation of groups within a molecule is especially important in the field of pharmacy. Despite the fact that two molecules resemble each other does not mean that they necessarily will act the same way in a certain type of drug. One of the forms can actually be harmful to the body, while the other one is benign and actually helps to cure problems. This is why it is important to be able to visualize the 3-D version of the molecule to make sure that the groups are placed in the right place in respect to the other groups located in the molecule. This is helped with the program of chemdraw as well as the Chem3D software. For this lab, the structure of butane was initially drawn. The four carbons were initially drawn on to the chemdraw panel using chem3D. From there different properties were found. First, the minimal energy was found which involves altering the bond angels between three of the four carbons. This minimal energy rotates the bond so that the position of the carbons with their R-groups are in a specific angle so that the minimal energy can be observed. This minimal energy is usually best when the largest groups are farthest away from each other to prevent steric hindrance. Of course with this there is a specific angle that the molecule is rotated to achieve the minimal energy. This was found using the dihedral function, which rotates different parts of the molecule until a specific angle is observed. This optimal angle is the angle in which the molecule will be the most stable. 3-D is not readily viewable so to transform the 3-D molecule into 2-D, newman projections are used. Newman projections involve the bond between two carbons. With these two carbons one carbon is usually placed on top of another carbon. The groups on the other hand can either be eclipsed, which means the group on the front carbon is blocking the group in the same position of the carbon in the back. The other position would be staggered in which the back carbon is rotated sixty degrees so now the groups are not so close to each other. This reduces electron repulsion. There are also two different types of staggered. The first type is called gauche which is when the largest groups are adjacent to one another. This is not energetically favored due to steric hindrance. The other more stable staggered form would be the anti conformation. This is when the two largest groups are 180 degrees apart from each other. The two groups are the farthest away they could be preventing electron repulsion or steric hindrance from occurring.

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