Molecular Shape and Polarity Lab Results and Discussion
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Molecular Shape and Polarity Lab Results and Discussion

Course Number: CHEM 2070, Fall 2008

College/University: Cornell

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Results and Discussion The shapes and polarities of several molecules were first determined by use of the VSEPR model and were then compared with the results obtained from using a computer software program known as Spartan which performs quantum mechanical calculations. A pharmaceutical drug molecule was then designed with the intention of the molecule having the capability to favorably react with a known receptor...

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and Results Discussion The shapes and polarities of several molecules were first determined by use of the VSEPR model and were then compared with the results obtained from using a computer software program known as Spartan which performs quantum mechanical calculations. A pharmaceutical drug molecule was then designed with the intention of the molecule having the capability to favorably react with a known receptor site. First, an ammonia molecule was built using Spartan. The program was then used to measure the bond length of each N-H bond in the ammonia molecule, the distance between two hydrogen atoms in the molecule, the H-N-H bond angle, and the N-H-H bond angle. All three N-H bonds were found to have lengths of 1.012 , and the distance between two hydrogen atoms was found to be 1.653 . All three H-N-H bond angles were found to be 109.47, and the N-H-H bond angle was found to be 35.26. Spartan was then used to optimize the ammonia molecule, meaning that the geometry for which the molecule has the lowest energy was determined. After optimizing the structure, the N-H bond lengths, H-N-H bond angles, the magnitude and direction of the molecules dipole moment, and the partial charges of the hydrogen atoms and the nitrogen atom were measured using the program. All three N-H bond lengths were found to be 1.003 , and the H-N-H bond angle was found to be 112.27. The magnitude of the dipole moment for the molecule was found to be 1.76 D. The dipole arrow pointed away from the hydrogen atoms. The partial charge of each hydrogen atom was 0.423, and the partial charge of the nitrogen atom was -1.267. Spartan was then used to build a model of SF4 and optimize the structure. The S-F bond lengths, FS-F bond angles, dipole moment magnitude and direction, and partial charges of the sulfur and fluorine atoms were measured and recorded. These measurements are shown in Table 1. Table 1: Bond lengths, bond angles, dipole moment magnitude and direction, and partial charges of atoms in SF4 molecule Prior to lab, the formal charges, bond angles, and dipole direction for CH3Cl, PCl5, and NO3- were predicted using the VSEPR model. These results are shown in Table 2. Table 2: Formal charges, approximate bond angles, and dipole direction for CH3Cl, PCl5, and NO3- according to VSEPR Model To verify the results obtained from using the VSEPR model, the structures of the three molecules were built and optimized using Spartan, and the bond lengths, bond angles, partial charges, and dipole moment magnitude and direction were determined. The results are shown in Table 3. Table 3: Bond lengths, bond angles, partial charges, and dipole moment magnitude and direction for CH3Cl, and PCl5, NO3- according to Spartan computer software program The hypothetical pharmaceutical drug molecule was then designed. It was determined prior to lab that the ideal drug molecule for the known receptor (Figure 6.5) would have a width close to, but no greater than 4.97 and a length close to, but no greater than 8.04 . Observing the receptor molecule diagram also showed that the ideal drug molecule would have partial negative charges at its two lengthwise ends, so as to allow it to attract to the slightly positive hydrogen atoms found on the receptor molecules surface. The ideal drug molecule would also have a partial positive charge on a widthwise end, so as to attract to the receptors slightly negative O-H group. With the ideal dimensions and polarity issues in mind, the pharmaceutical drug molecule was constructed by building a pentane molecule using Spartan, and then continually adding and deleting atoms. The molecule was continually revised until an optimized molecule of 8.006 in length and 4.88 in width was created. Lengthwise, the molecule had an oxygen atom at each end, providing slight negative charge. Widthwise, the molecule had a hydrogen atom at one end, providing slight positive charge. The molecules structure is shown in Figure 1: Figure 1: My groups hypothetical drug molecule Percent error was calculated to quantify how strong of a match the dimensions of the hypothetical drug molecule are to the dimensions ideal for the receptor. The percent error calculation for the length is as follows: accepted value - experimental value Percent Error = accepted value 8.04 8.006 Percent Error = 8.04 Percent Error = 0.4 % The percent error was also calculated for the width and was found to be 2 %. These percent error values are very close to zero and thus suggest a very high degree of accuracy. Data from another lab group was recorded. Their hypothetical drug molecule had a length of 7.558 and a width of 3.822 . Lengthwise, the molecule had an oxygen atom at each end, providing slight negative charge. Widthwise, the molecule had a hydrogen atom at one end, providing slight positive charge. The molecules structure is shown in Figure 2: x 100 x 100 Figure 2: Other groups hypothetical drug molecule Percent error was calculated to quantify how strong of a match the dimensions of the other groups hypothetical drug molecule are to the dimensions ideal for the receptor. The percent error for the length was found to be 6.0 %, and the percent error for the width was found to be 23.1 %. The percent error for the length suggests relatively high accuracy, while the percent error for the width suggests a relative lack of accuracy.

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