8/05: J.A.P, rev. 1/08:W.L.HMolecular Modeling: Visualizing Molecular Shape and PolarityII. Outline of the process for running SPARTANControls for moving and rotating molecules on canvas: (If more than one molecule is on the canvas select the desired one by left clicking on any atom. The name of the selected molecule will appear in the lower right hand corner.)III. Molecular GeometryA. 3-D Shapes from Lewis StructuresC. Effect of Lone Pairs on VSEPR Bond AnglesD. Molecules with “Expanded Octets”IV. Polarity: Bond Dipoles and Dipole MomentsB. Dipole MomentsRecall again that for the molecule as a whole to be polar, two things must hold true. First, it must have polar bonds. But also, the symmetry of the molecule must be such that polarity of the individual bonds (the bond dipoles) does not cancel out. To illustrate this point, we’ll divert our attention to a couple of other molecules BF3 and PF3. (In the meantime you can close H2O, NH3 and CH4, or move them to the side). Build both BF3, and PF3 (It will save to time to draw a Lewis structure, and start from the correct VSEPR geometry). As before, calculate the equilibrium geometries, and calculate the ‘size’ density and ‘bond’ density surfaces with the ‘potential’ mapped onto them.Cleanup8/05: J.A.P, rev. 1/08:W.L.HMolecular Modeling: Visualizing Molecular Shape and Polarity(Using Spartan on PC computers)I. IntroductionThe goal of this lab is to utilize molecular modeling software to assist you in building the following skills. After completing this exercise you should be able to:• Use VSEPR to predict the electron pair geometry and molecular geometry for a given molecule based on its Lewis Structure, and sketch its 3D shape.• Classify a molecule as either “polar” or “non-polar” according to its shape and the polarity of its individual bonds.The field of molecular modeling, or more broadly, computational chemistry, refers to investigating molecules strictly through calculations. It has grown rapidly in the past two decades, primarily because advances in computing speed have enabled the use of very sophisticated (quantum mechanical) models to simulate the electron distributions of molecules. The field has had such a broad impact on chemistry that the 1998 Nobel Prize in Chemistry was awarded to a pair of individuals who were instrumental in developing efficientnumerical procedures to execute such calculations. Today, a substantial fraction of chemists are exploiting computational methods for their research, and such methods are even making their way into introductory chemistry courses… The plan for this lab exercise is to learn the basics of the program by “building” and simulating a few simple molecules that you are quite familiar with. At the same time, you will be drawing Lewis Structures and predicting the geometries of these molecules using VSEPR (Valence Shell Electron Pair Repulsion) Theory. The basis of VSEPR theory is that the electron pairs about a given atom move away from each other as far as possible to minimize the repulsive forces between them (all are negatively charged). As a result, for a given number of electron pairs about a given atom (either bonds or lone pairs), there is a standard arrangement called the electron pair geometry. This dictates the overall shape, and the values of the bond angles. After considering the lone pairs, and their effect on the geometry, we then focus strictly on the atoms and bonds when we specify the molecular geometry. This is the actual shape of the molecule, but it is critical to first consider the lonepairs and their effect on the structure. At the end of this document there are some appendicesthat describe electron pair geometry, molecular geometry, and guidelines for drawing Lewis Structures. Our investigation of shapes will conclude with an examination of molecules with more than 8 electrons about the central atom.Modeling (PC) - 1After investigating shape, we will then exploit the graphical capabilities of SPARTAN to illustrate “polar” bonds. Then, we will combine this insight with that that we have gained regarding shape and learn to predict whether or not a given molecule is polar – as a whole. If so, we say it has a dipole moment. This quantity is real and measurable, and its magnitude indicates the degree of charge separation in the molecule. NOTE: You may need some scratch paper for preliminary sketches of Lewis structures and VSEPR geometries. Questions to be answered are in bold, and are separated from the body of the text. Others embedded in the text (and usually in italics) are to provoke thought. II. Outline of the process for running SPARTANThe process for modeling molecules in SPARTAN follows the same general outline:a. Build a molecule: Use the mouse to make bonds in an arrangement that is your “best guess” as to how the atoms are arranged. This shape is just the initial guess, however.b. Calculate and minimize molecular energy: SPARTAN next adjusts atom positions and the electron distribution in the molecule to find the lowest energy structure and electron distribution. This is the real power of this program. Sophisticated quantum-mechanical models are used to obtain a refined view the “best” structure. c. Calculate surfaces: There are some powerful visualization capabilities as well. “Electron density surfaces” will be used to better envision shape, and charge distribution (to better envision polarity) can be plotted directly on these surfaces with color-coded scheme.SPARTAN allows for a wide range of molecule shapes and bonding, i.e. you can build almostanything, but just because the program will let you build it doesn’t mean that your molecule isstable. Step “b.” is crucial (do not try to answer questions below without running the calculations). During step “b.”, three different things could happen:i. The program returns a structure with the same general shape (the bond lengths and angles may have changed a bit). But it is not necessarily the best structure. You will need to examine the energy values for all stable structures to determine which is “best”. (More on this below. See footnote #3 for a thorough clarification).ii. The program returns a structure with a completely different shape, which means that your starting structure was something of a poor guess.iii. The calculation takes a long time, and the structure it returns is not bonded at all – the