NAME: __________________ Lab Day/Time: ________________Molecular Modeling BV 1/2009PurposeThe purposes of this experiment are:To learn how to use molecular modeling software, a commonly used tool in the chemical and pharmaceutical industry.To examine the structures of a number of simple molecules to search for common factors affecting molecular structure.ProcedureThere are a variety of software programs available to perform molecular modeling experiments, with names such as Spartan, Mopac, and Gaussian. The one we use is CAChe, and we have a “site license” for it. This means that, although a single copy costs upwards of $1,000, each of you can install a copy onyour own computer and use it at will.In this experiment you will learn how to: - “build” molecules in the program- analyze bond lengths- analyze bond angles- analyze torsion angles- use these skills to perform an analysis of the structures of a series of small molecules.Prelab AssignmentBefore coming to lab, fill in the Lewis structures in Tables 1, 2A, 2B, and 4.Determine the formal charges and oxidation numbers requested in Table 4.How to Use CAChe/Scigress1. Building MoleculesRun Workspace from either the CAChe or Scigress folders in All Programs. If a query comes up the first time, just say yes.Choose New if a workspace window does not come up. Use the Drawing Pencil to sketch out your molecule. - To add the first atom, select the element and click in the middle of the workspace. - To add addition atoms, select the element and then click-and-drag from the element you want it bonded to.- To make a double or triple bond, either drag again between the two atoms, or use the Select tool to select the bond and change the drop-down menu to change it.- Once complete, finalize the molecule using Beautify/Comprehensive, or Ctrl-B.2. Performing Advanced Calculations (Experiments)Save the molecule using a name of your choice.Choose the Experiment/New.Select the Property to be determined. Popular selections are “HOMO-5 to LUMO+4” and “electrostaticpotential on electron density.”Click Start and wait for the calculation to run its course. For small molecules this is usually less than 10 seconds.Close the Experiment windows.3. Making MeasurementsBond Length: select the two bonded atoms using the Select tool. Click on one atom, hold down shift, and click on the second atom. Then choose Adjust/Atom Distance, or press F2. The units used are Angstroms. 1 A = 10-10 m, or 10-8 cm.Bond Angle: select three atoms- in order with the central atom second. Then choose Adjust/Bond Angle.Torsion Angle: select four atoms- in order following the bonding linkages. Then choose Adjust/Torsion Angle.Partial Charge: Build the molecule and save it. Run Experiment/New/Property = current energy. When the calculation is done, choose View/Atom Attributes/Label/Partial Charge. The numbers will be seen with the atoms. You’ll probably need to rotate the molecule to see them.Experiment #1. What controls bond length?For each molecule, draw the Lewis structure, build the molecule, beautify it, and measure the bond lengths indicated.Formula Lewis Structure Bond lengths to measure:CH4C-HCH3F C-FCH3Cl C-ClCH3Br C-BrCH3OH C-HO-HCH3NH2C-HN-HCH3CH3C-CCH2CH2C-CCHCH C-CPart 1. Questions:1a. What are the two factors that control bond length?1b. Which of these has the largest effect on bond length?1c. Given your ideas, design a molecule on paper that contains specific bonds you have not yet measured. For example, you could make a molecule that contained a S-F bond, or a P-Cl bond. Predict the bond length and then test your prediction using CAChe. Formula Lewis Structure Predicted Bond Length Measured Bond LengthWhich bond:Length:Experiment #2. What controls bond angle?We have learned that the angle between two bonds depends mainly on electron-pair geometry of the central atom, which in turn depends on the number of structurally important electron pairs on the central atom. Confirm this by again drawing the Lewis structures for the following molecules and then analyzing the indicated bond angles in CAChe. Build the molecule and choose Beautify/Comprehensive.When viewing the molecules in CAChe, also view the positions of the lone pair electrons by selecting View/Show Electrons.Part 2a. Control via number of Structural Electron PairsFormula Lewis Structure Number of StructurePairsBond AngleCH3CN On central C: C-C-N:BF3B: F-B-F:CH2O C: H-C-H:CH4C: H-C-H:PF5F: F-P-F:SF6S: F-S-F:Part 2b. Control via Number of Lone Electron PairsThe following three measurements need a more exact calculation of molecular shape. CAChe uses the most simple hybrid orbital/VSEPR rules to create structures when “beautifying.” In order to obtain a more accurate shape for the molecule, you must Save the built and beautified molecule and then optimize the geometry using Experiment/New/Property = optimized geometry. Formula Lewis Structure Number of StructurePairsNumber of Lone Pairs on Central AtomBond AngleCH4C: H-C-H:NH3N: H-N-H:H2O O: H-O-H:Part 2. Questions2a. Does the number of structural pairs on the central atom control bond angles around that atom?yes or no2b. Compare BF3 and CH2O. Each has a central atom with 3 structural pairs, but the C in CH2O has a total of 4 bonds whereas B in BF3 has only three bonds. Which matters more about the central atom: the number of structural pairs or the number of total bonds2c. Now consider the bond angles in Part 2b. In effect, the trend going from CH4 to NH3 to H2O is to replace a bonded H atom with a lone pair. What effect does that have on the bond angles?2d. Give a reason why the trend you state in Question 2c occurs.Experiment #3. Torsion (Dihedral) angles.When a series of atoms are connected together, their relative positions are referred to as a conformation. Conformations describe twisting of one part of the molecules with respect to another. The easiest way to observe this is to examine atoms bonded to adjacent central atoms and see if they line up (they are eclipsed) or seem to avoid each other (they are staggered). Build and Beautify the molecules below and describe the manner in which the outermost atoms line up, or don’t.Lewis Structure and torsion to measure.Describe the relative positions ofthe outermost atoms.Part 3. QuestionsThere are two factors that might control how one fragment of a molecule will twist with respect to another fragment. Steric Hinderance: This comes about when atoms just get in each other’s way and