Moleular Modelling

Bob Lee September 24, 2012

Hong Zhao Section 248

Introduction to Molecular Modeling

ABSTRACT

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.

INTRODUCTION

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.

METHODS / PROCEDURES

The methods and procedures for this specific lab was all listed on the handout in which an explanation of how to use chemdraw and chem3D was written.

RESULTS

After drawing the butane molecule, the minimal energy calculation was performed. The minimal energy of butane that was obtained was 2.192 kcal/mol. The bond angle that was found between the three carbons was 119.9029 degrees. However, the optimal angle for this butane was 109.5000 degrees. From the single angle plot generated by the dihedral driver function, it was visible that there were major energy differences and that the graph was symmetrical. Clicking around the graph, it was visible that the higher energy is associated with smaller angles while lower energies are usually associated with larger angles. From the photos attached, it is clear that the energy differences can be associated with the orientation of the molecule when drawn with the newman projection. When the molecules were farther apart meaning when the groups weren't as close to one another the energy seemed to be lower. However, as the groups were pulled closer together the energy seemed to drastically increase. Similar results were found when trying to find information for 2-methylbutane. However the initial minimal energy was somewhat higher with a value of 3.6254 kcal / mol. The actual bond angle that was between the first three carbons was 110.2664 degrees while the optimal angle was fairly close with a value of 109.5100. However, comparing the 2-methylbutane as well as the ordinary butane, the energy diagram differed. The energy diagram differed in that the energy points within the graph of the 2-methylbutane were higher at most points.

The errors that could have arose from this experiment all involved the chemdraw program. The results seems to be plausible in that there is an extra carbon in the 2-methylbutane resulting in a higher energy molecule meaning that the chart would be more extensive and some points will be higher. However, the molecule for 2-methylbutane could have been drawn in that the carbon coming off the second carbon may actually have not been attached at all and the data chart might not have been altered to match the actually 2-methylbutane molecule. Some of the data might not have been recorded incorrectly. This could have resulted from interpreting the graph incorrectly, using the wrong bond angle measurement after performing the dihedral calculation, or the minimum energy might have been either too high or too low.

DISCUSSION

Looking at the energy graph for the general butane molecule there are varying highpoints as well lowpoints. The highest point on the graph for the butane molecule is when the molecule was at zero degrees. This reason comes from the fact that the groups are really close to each other causing electron repulsion Since this is the highest energy, the newman projection for this particular energy must be in the eclipsed form. Specifically the eclipsed form has the two methyl groups next to each other. Since these two groups are the biggest groups attached to each carbon, having them next to each other not only causes