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Laboratory 5: Molecular Modeling with Spartan Flipbook PDF
Laboratory 5: Molecular Modeling with Spartan In this lab you will gain additional practice in thinking about molecular
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Laboratory 5: Molecular Modeling with Spartan In this lab you will gain additional practice in thinking about molecular geometry using a sophisticated molecular modeling software program to create and optimize structures. Although you can save your work electronically, it still is a good idea to record information in your lab notebook. When saving files, make sure you save them to your P: drive or a flash drive–all files saved to the desktop or the documents folder are deleted whenever the computer is restarted! You have already found that it is easy to predict the geometry of a molecule or ion by using VSEPR theory. While this is an excellent approach for predicting the geometry around a central atom, it cannot provide more detailed quantitative information such as exact bond lengths and bond angles. Molecular modeling programs accomplish this by using classical mechanics (Coulomb’s law) and/or quantum mechanics (Schrödinger’s wave equation) to optimize the geometry, including bond lengths and angles, and overall energy. In this experiment you will use the popular molecular modeling program Spartan to investigate the structure of some inorganic molecules and ions. You will compare the more quantitative results of your calculation with that of the simple VSEPR model you are using in class. Pre-lab Assignment –
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Please draw, in your lab notebook, a valid Lewis dot structure for PF6 and NO3 . In addition, use VSEPR to predict the geometry for each ion and then sketch a threedimensional picture for each ion. Procedural Details We will meet in the Chemistry Computer Lab, which is in Julian 340. Your instructor will provide a hands-on demonstration of Spartan at the beginning of the laboratory period. You will work with one partner on this lab, dividing the work in whatever way you wish, provided that each of you complete some of the work with Spartan. You may work on the lab at any time that is convenient for you and your partner; however, you may wish to stick around for the remainder of the lab period while your instructor is available for questions. The computer lab is open 8 am to 5 pm every day and is also is open on the following evenings from 7 pm to 10 pm: Sun, Mon, Tue, Wed, Thurs.
Chem 130 Fall 2007
Molecular Modeling Exercises Read through each of the following molecular modeling exercises. Before coming to lab, it would be extremely helpful to draw Lewis structures and to use VSEPR to predict geometries, including bond angles and relative bond lengths (e.g. the bond angle XAX is less than 90° or bond AB will be longer than bond AC). This will help you determine whether Spartan’s calculations make sense or if there is a possible mistake in your calculations! 1. The ion and molecules NH4+, NH3, N(CH3)3 and H2O all have the same number of electron domains (and, therefore, the same electron domain geometry) with different numbers of lone pairs. Use Spartan to optimize the structure for each and measure all bond angles. Describe how the angles vary through this series. What does this imply, in light of the VSEPR model, about the relative size of the lone pairs and the various other groups bound to the central atom in this series? Are your results from the calculation consistent with what you know about periodic trends and the sizes of atoms? 2. As shown below, the trigonal bipyramidal geometry has two unique positions around the central atom: axial and equatorial
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equatorial
As a result, molecules with this electron domain geometry can, in principle, have several different structures. Consider the molecule SF4. How many possible arrangements are there for the four fluorine atoms? Carefully draw each unique possibility (if you can rotate a structure around to form one you’ve already made it isn’t unique!). Optimize each of the unique structures in Spartan. Which of the geometries does Spartan predict to be the most stable? Does it agree with the one predicted by VSEPR? Explain why this is the most stable structure. 3. Use Spartan to find optimum structures for PBr5, PCl5, and PI5 and measure all bond lengths for each molecule. In light of your understanding of VSEPR and of the relative repulsions of atoms in different positions, do the relative bond lengths within each molecule make sense? Explain. Do the relative bond lengths between the three molecules make sense? Explain.
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Chem 130 Fall 2007 4. The compounds listed below have the general formula PF3R, where R is a variable group. Optimize the structure for each of these compounds. Based on your results, rank the R groups from largest to smallest (you will need to think carefully about what property to compare for all species!). Explain your reasoning in terms of the VSEPR model and what properties you decided to compare. +
PF4 PF3 PF3O PF3S PF3CH2
R=F R = lone pair R = O (double bonded) R = S (double bonded) R = CH2 (double bonded to the carbon) –
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5. The oxo anions of chlorine are ClO , ClO2 , ClO3 , and ClO4 . All have geometries based upon a tetrahedral orientation of electron domains. Draw valid resonance structures for each ion and predict the relative O-Cl bond order for each. Use Spartan to find the optimum structure for each of these ions. According to your simulation, which ion has the highest Cl-O bond order (based on bond length)? Is this consistent with your predictions? If your answer is no, then draw inequivalent resonance structures that better support Spartan’s predictions. –
6. Consider the oxo anions SiO44-, SO42-, PO43-, and ClO4 . Draw valid resonance structures for each of the anions and predict the expected geometry for each. Use Spartan to find the optimum structure for each of these ions. According to your simulation, which ion has the longest X-O bond? Is this consistent with what you would predict using the sizes of the central atoms? Is it consistent with the bond orders predicted by your resonance structures? Explain. Final Report Complete all of the molecular modeling exercises before writing the report. Your report for each exercise should begin on a separate page and include three parts: pre-lab work, results from Spartan, and discussion. Begin each exercise by drawing Lewis structures, including resonance structures where relevant, and predictions about bonding geometries, including bond angles. Where appropriate, include predictions about relative bond lengths and bond orders. Next, gather together your results from Spartan, using tables to organize your data; be sure to include only that data relevant to the exercise. Finally, answer the questions in each exercise in the form of a well-written narrative. You should expect that the results of some calculations will conflict with your predications; try to offer a reason for such discrepancies. Turn in one copy of your report for your group, which should be a joint effort; your signature on the report indicates that you contributed to and are satisfied with the report. 3