Chemistry Report #6, Molecular Shape and Polarity

Chemistry Report #6, Molecular Shape and Polarity -...

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Molecular Shape and Polarity By Amanda Koszewski TA: Deepti Gadi October 31, 2006
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Results and Discussion: In order to become familiar with the details of the Spartan software program, models of ammonia and the nitrate anion were built and manipulated. The molecular shapes and polarities of CHCl 3 , PF 5 , and SO 3 2- were determined to verify predictions made using the VSEPR model. Finally, a drug molecule believed to bind with a hypothetical receptor was designed. Part A- Learning to use the software After building and manipulating the ammonia and nitrate anion, bond lengths and angles were measured. The experimental results were tabulated (Table 1): Table 1: Ammonia and Nitrate Anion Measurements Prior to Optimization Molecule Bond Bond Length (Ǻ) Bond Bond Angle (°) Molecular Structure NH 3 N-H 1.012 H-N-H 109.47 N-H 1.012 H-N-H 109.47 N-H 1.012 H-N-H 109.47 N-H-H 35.260 NO 3 - O=N 1.30 O=N-O 120.00 O-N 1.48 O-N-O 120.00 O-N 1.48 O-N=O 120.00 The distance between two hydrogen atoms was also measured at 1.653 Å. Following, both structures were optimized to achieve a molecular shape particular to the specific forces acting within the molecule or ion. By optimizing each structure, the geometry of lowest energy could be determined. Bond lengths and angles for each structure were measured once again after being optimized to detect any changes that may have occurred. The polarity and partial charges of ammonia and the nitrate anion were also measured (Table 2):
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Table 2: Table 2: Optimized Ammonia and Nitrate Anion Measurements After optimizing the ammonia molecule, the N-H bond lengths decreased from 1.012Å to 1.003Å. The H-N-H bond angles were slightly smaller at 107.21° when optimized as opposed to the 109.47° angles when not optimized. The less-than-tetrahedral bond angles can be explained by the fact that the charge cloud of the lone-pair electrons spreads out. This forces the bond-pair electrons closer together and reduces the bond angles. Ammonia’s molecular geometry was determined to be trigonal pyramidal and the molecule was polar. The magnitude of the dipole moment was 1.92 debye and the arrow pointed towards the lone pair on top of the nitrogen atom. The partial charges also indicated the direction of the dipole moment. The electronegative nitrogen atom acquired the negative partial charge while the hydrogen atoms had a positive partial charge. Since dipole moments point in the direction of negative charge, the dipole moment of ammonia was directed towards the nitrogen atom. Similarly, the molecular geometry of the nitrate anion was determined to be trigonal
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Chemistry Report #6, Molecular Shape and Polarity -...

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