6: Experiment Molecular Shape and Polarity By Chris Bostick Lab Instructor Chris Sgro October 28, 2005
Results and Discussions: The goal of this experiment was to compare predictions based on VSEPR model with quantum mechanical calculations to determine the shape and polarity of a number of molecules. Using predictions based on VSEPR prior to the lab, a comparison was taken using quantum mechanical calculations on a computer program called CAChe. Using all of this information, a drug was constructed to react with the model presented in Figure 6.1 in the lab book. Part A The program was tested using NH3 and NO3- as examples. After building NH3 using the tools, it was necessary to use Beautify | Comprehensive to force the bond angles to achieve the ideal value for the central atom. The angle was similar to the VSEPR prediction. Then the length of the bonds were measured and found to be equal to the information given in Table 3.1 in the lab book. The following measurements were the ones obtained before optimization. NH3 Model Atoms H-N-H Atoms N-H H-H
Bond Angle 109.47 degrees Bond Length 1.02 Angstroms 1.67 Angstroms
After the figure was optimized under "optimized geometry" settings the following measures were obtained. Atoms H-N-H Atoms N-H Bond Angle 106.9 degrees Bond Length 1.014 Angstrom
The following partial charges were obtained using View | Partial Chg & Calc. Bond Order. Atoms Partial Charge H .246 C -.738 NO3- model After beautifying the model the following measurements were obtained. Atoms O-N=O O-N-O Bond Angle 120.001 degrees 119.97 degrees
Atoms N-O N=O
Bond Length 1.48 Angstroms 1.299 Angstroms
After Optimizing the following measurements were taken. Atoms O-N=O O-N-O Atoms N-O N=O Partial Charges measured: Atoms N O Part B: The following measurements for CH2Cl2 were taken using CAChe. Partial Charge 2.032 -1.011 Bond Angles 120.001 degrees 119.97 degrees Bond Lengths 1.212 Angstroms 1.211 Angstroms
Atoms H-C-Cl H-C-H Cl-C-Cl Atoms H-C C-Cl Atoms Cl H C
Bond Angles 109.472 degrees 109.471 degrees 111.869 degrees Bond Lengths 1.0900 Angstroms 1.76 Angstroms Partial Charges -.214 -.012 .453
The VSEPR model predicted prior to the lab for CH2Cl2 was a Tetrahedral with bond angles of 109.5 and partial charges predicted to be neutral. The bond measurements are close enough to VSEPR to not discredit it. The partial charges are all very small and in significant to disproving VSEPR. The suggested bond lengths in Table 3.1 were very close to the ones observed in the experiment. H-C 1.09 Angstroms and C-Cl 1.77 Angstroms.
The following measurements were taken for SO3Atoms O-S-O Atoms O-S Atoms S O Bond Angle 94.247 degrees Bond Length 1.75 Angstroms Partial Charge 2.161 -1.387
Discrepancies are the angle measurement and the partial on charge sulfur. The angle measurement can be explained by the fact that VSEPR model doesn't properly take into account the effect of the lone pair found on sulfur. The lone pair pushes down the oxygen's bonded lowering the angle from 109.5 to 94.247. VSEPR model shows a charge of +1, but the CAChe shows a charge of +2. The bond length suggested in Table 3.1 for S-O is 1.51 Angstroms which is not significantly different from 1.75 Angstroms. Part C: To design a drug that would be effective with the reactive space in Figure 6.1, the length and width of the receptor space was calculated using bond lengths. Length = 9.29 Angstroms Width = 4.97 Angstroms The total length and width of the designed drug should not exceed these parameters, and they should be within 1 Angstrom for the drug to be effective. The drug created to fit these parameters was C5H10O7 . The following measurements are of C5H10O7. Atoms H-O-C C-C-C H-C-H Atoms H-O C-O C-H C-C Total Length 8.929 Angstroms Bond Angle 104.49 degrees 109.42 degrees 109.42 degrees Bond Length .95 Angstroms 1.50 Angstroms 1.09 Angstroms 1.54 Angstroms Total Width 4.495 Angstroms
The Partial Charges measured were small and insignificant to proving the effectiveness of the drug. The total length of the drug has a difference of .361 Angstroms from that of the
receptor site ensuring reactivity between the functional groups. On the left side Hydrogen would be bonding with Hydrogen, Table 3.1 gives an H-H bond length of .74 Angstroms. The distance between the two Hydrogen's is less then that making it reaction probable. On the right side Hydrogen would bond with Oxygen. Table 3.1 gives the length of an OH bond to be .96, thus since the distance is less then that a reaction is probable. The total width of the drug has a difference of .475 from the width of the receptor site, ensuring a reaction. A Hydrogen would be bonding with an Oxygen at the bottom with a bond length suggested to be no farther then .96. The angles of 109.42 and 104.49 angle it towards the receptor sites functional groups opposed to angling them away. The comparative group's drug is C7H4O with a total length of 9.629 Angstroms and a total width of 3.27 Angstroms. The length exceeds the receptor site but would possibly still be able to react to some degree. However the difference between their width and the total width is 1.7 Angstroms which is possibly to far for a reaction to take place. Conclusion: lOur drug would prove more reactive because of the better fitting into the receptor site, and minimal distances between functional groups. Analyzing the effectiveness of VESPR, it is observed that it is for the most part accurate in its predictions. Minor discrepancies appeared considering lone pairs, but not enough to completely falsify VSEPR predictions.