11. MOLECULAR MODELINGChemists frequently use models to better understand chemical phenomena. In this laboratory modelsare used to analyze chemical bonding and molecular structure. We will start with the Lewis electron dot(Localized Electron) model1 and use it to predict the electronic structure of some simple molecules. Wewill then use ball-and-stick models to construct three-dimensional models of those molecules. Thethree-dimensional models will be refined using Gillespie’s Valence Shell Electron Pair Repulsion(VSEPR) model2. Finally, we will use Spartan3, a computational chemistry program, to calculate themolecular geometry. The results from Spartan will then be compared with the VSEPR results. Computational chemistry. In theory, all of chemistry can be understood as solutions of Schrödinger’swave equation. In practice, solution of the Schrödinger equation is so complicated that chemicallyaccurate calculations for molecules involving more than three electrons and three nuclei, e.g. H3, arebeyond the reach of current computer hardware/algorithms. To model the properties of larger (andmore interesting) molecules, chemists must use some form of approximate computational method.The simplest, and thus fastest, computational method is called molecular mechanics. In molecularmechanics the bonds of a molecule are treated as springs and the force constants of the springs aredetermined from experimental measurements. The overall molecular energy is the sum of the energiesof stretching, bending and torsion (the molecular force field) for all of the bonds in the molecule.Although molecular mechanics ignores electronic properties, it gives quite good structural results forlarge molecules such as proteins. Drug companies performed much of the pioneering work onmolecular mechanics. Spartan uses a molecular mechanics program called MMFF (for MerckMolecular Force Field) developed by Merck Pharmaceuticals and one called SYBYL developed byTripos, Inc., a St. Louis drug discovery company. Semi-empirical molecular orbital methods are the next level of computational accuracy. Semi-empirical methods take advantage of the fact that some of the quantities that are hardest to calculatecontribute very little to molecular energy. They can thus be ignored without a significant loss ofaccuracy. Other hard-to-calculate quantities can be replaced by experimental values. There is averitable alphabet soup of semi-empirical methods. Spartan uses MNDO (Modified Neglect of DiatomicOverlap), AM1 (Austin Model 1) and PM3 (Parametric Model 3). All three were developed by M. J. S.Dewar’s research group at the University of Texas, Austin between 1975 and 1990. Each method hasits own strengths and weaknesses. A lot of semi-empirical computational chemistry involves decidingwhich model works best for the problem you’re working on. In this laboratory, we will use AM1. At a higher level of computational accuracy is the Hartree-Fock molecular orbital method. This wasdeveloped in the 1930s by Douglas Hartree, a British mathematician and Vladimir Fock, a Russianphysicist, but was not widely used until digital computers became available in the 1960s. We will not beusing the Hartree-Fock method, but when you get to the Calculations… screen in Spartan’s Setupmenu, you will see Hartree-Fock listed as one of the choices. To put this in perspective, for a molecule like SF6, a molecular mechanics calculation takes about onesecond, a semi-empirical calculation takes about five seconds and a Hartree-Fock calculation takesseveral minutes. Molecular mechanics does not give molecular energies but can do a reasonable job ofpredicting which molecular arrangement is most stable. Semi-empirical methods can calculatemolecular energies to an accuracy of a few percent, while Hartree-Fock calculations give molecularenergies accurate to a few tenths of a percent. The difficulty is that most chemical problems, such aspredicting the path of a reaction, require accuracy of ~10-3 percent. Computational procedures that canwork at this accuracy are available, but they are very complex and computationally intensive. PROCEDURE - Your report will consist of the attached worksheet, which lists ten molecules that youwill study. For each molecule:1. Write the Lewis electron dot structure, 2. Using the “ball-and-stick” model kit, construct a 3-dimensional model,23. Sketch the shape of the molecule, including lone pairs, and name the molecular shape.4. Draw the molecule in Spartan (two examples are given below to illustrate the procedure) andmeasure the VSEPR model bond angles as discussed in the paragraph on the water molecule. 5. Log onto your server space (F: drive) and create a folder in which to save your molecularmodels, Set up and carry out the AM1 calculations in Spartan as follows to find the most stablestructure and measure the theoretical bond angles, then compare them to the experimentalbond angles listed on the work sheet. To carry out the calculations:• When you are ready to calculate the structure, Select Calculations… from the Setup menu.In the Calculate: block, select Eqilibrium Geometry with Semi-Empirical and AM1. • In the Start from: block, select Initial geometry. • In the Subject to: block, check Symmetry. • The Total Charge should be Neutral unless the species has a net charge, in which case setit to the appropriate charge. The Multiplicity should be Singlet. • In the Compute block, check Elect Charges. • Check Global Calculations. • Click on Submit. Spartan will prompt you to save your model. After saving the model, awindow will open notifying you that Spartan has started. Click on OK to close that window.After 5 – 30 seconds, a window will open notifying you that Spartan has completed. Click onOK to close that window and you will see the calculated equilibrium geometry of themolecule. After completing all of the molecules, answer the following questions on the back of the report form.6. From your knowledge of electronic structure, explain any differences between the bond anglespredicted by the VSEPR model and those predicted by Spartan, 7. For the molecules H2O and H2S, comment on the effect upon bond angles of changing theelectronegativity of the central atom. Can this be explained using the idea of electron-pairrepulsion? 8. In a similar manner, explain the trend in bond angles for the series PF3, PCl3, and PBr3. Doesatomic radius or electronegativity seem to play a role?Your lab report