Molecular Modeling PDF

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Professor: Gita Venkatakrishnan...

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Molecular Modelling- E2 Reactions Abstract The purpose in conducting this lab was to gain a better understanding of racemic mixtures as well as E2 reactions. This was done through the use of Chem3D and ChemDraw which visualize molecules in a 3 dimensional manner. Using these programs, the minimized energies of molecules were able to be determined as well as their properties. The minimized energies were as follows: 2.8187 kcal/mole (1-Butene), 2.6150 kcal/mole (cis-2-butene), 2.1823 kcal/mole (trans-2-butene), and 3.3960 kcal/mole (2-bromobutane). The energy of 2bromobutane was then tested for varying conformations. The starting conformation had an energy of 3.396 kcal/mole. After rotating 60 degrees around the 2-3 carbon bond, the conformation had an energy of 7.856 kcal/mole. After another 60 degrees, the energy decreased to 5.641 kcal/mole. At 180 degrees of rotation, the energy of the conformation was 11.004 kcal/mole. The final two rotations offered energies of 5.115 kcal/mole and 12.092 kcal/mole at 240 degrees and 300 degrees respectively. Data 1-Butene

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Minimized Energy: 2.8187 kcal/mole

Trans-2-butene

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Minimized Energy: 2.1823 kcal/mole

Cis-2-butene

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Minimized Energy: 2.6150 kcal/mole

2-bromobutane

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Minimized Energy: 3.3960 kcal/mole

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Conformational Energy: 3.396 kcal/mole

Line Bond Structure: 0-120 degrees

Line Bond Structure: 180-300 degrees

Newman Projections

Table 1: Conformational Energies Degrees of Rotation Around Central Bond Energy per Conformation (kcal/mole) 0 3.396 60 7.856 120 5.641 180 11.004 240 5.115 300 12.092 360 3.396

Rational Energy Diagram

Energy (kcal/mole)

13 12 11 10 9 8 7 6 5 4 3

0

50

100

150

200

250

300

350

400

Degrees of Rotation Around Center Bond

Questions 1. The line bond structures above are related to the Newman projections for each conformation of the molecule. Though the Newman projections differ, the line bond structure does not change. 2. The ratio of the syn-periplanar conformation to the anti-periplanar conformation is calculated to be 0.6020. This ratio can be related to the predominance of the trans alkene by seeing this ratio as a percentage. The estimated yield of the trans alkene is 60% and this ratio also proves this, therefore the ratio is a one to one system that can be used to determine the percent yield of different substances. 3. The ratios of the anti-periplanar conformation to the cis and trans conformations is calculated to be 0.4322. Dividing this by 2 gives the expected approximate 20% yield of the cis conformation.

4. The changes in energy from 0 degrees to 60 degrees, 120 degrees, and 180 degrees can each be calculated. In this experiment, the change in energy was found to be 4.460, 2.245, and 7.608 kcal/mole respectively. These values however are unsuitable for describing product distribution because it does not highlight the abundance of these conformations. 5. See figure above in data section. Conclusions In this lab, the purpose was to experiment with different conformations of 2-bromobutane in order to determine the relative energies for each conformation. In determining the minimized energies, trans-2-butene carried the least energy with 2.1823 kcal/mole and 2-bromobutane carried the most energy with 3.3960 kcal/mole. This refers to the overall stability of the molecules and makes sense that trans-2-butene would have a smaller energy than 2-bromobutane because it is much more stable. In the case of 2-bromobutane, however, there are a number of conformations in which the molecule can exist, each carrying different amounts of energy based on their stability. The least stable or highest energy conformation of the molecule was found at a 300 degree rotation around the central bond between carbon 2 and 3 with 12.092 kcal/mole. The most stable or least energy conformation was found at the starting conformation of 0 degrees with 3.396 kcal/mole. In the rational energy diagram above, the relationship between energy and degrees of rotation is shown. From those values, the relative abundance of the conformations could be could be calculated and confirmed....