The Use of Molecular Modeling as “Pseudoexperimental” Data for

Jul 30, 2015 - This exercise can be completed by first-semester general chemistry students in a 3-h time period and without the need for students to l...
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The Use of Molecular Modeling as “Pseudoexperimental” Data for Teaching VSEPR as a Hands-On General Chemistry Activity Christopher B. Martin,* Crissie Vandehoef, and Allison Cook Department of Chemistry and Biochemistry, Lamar University, Beaumont, Texas 77710, United States S Supporting Information *

ABSTRACT: A hands-on activity appropriate for first-semester general chemistry students is presented that combines traditional VSEPR methods of predicting molecular geometries with introductory use of molecular modeling. Students analyze a series of previously calculated output files consisting of several molecules each in various geometries. Each structure is analyzed with respect to the calculated relative energies and bond angles and then compared to the predicted geometry obtained using VSEPR theory. Therefore, students gain exposure to and an introductory experience in computational chemistry, while reinforcing the connection between VSEPR theory and “pseudoexperimental” results obtained from the calculations. This exercise can be completed by first-semester general chemistry students in a 3-h time period and without the need for students to learn how to actually perform the calculation themselves. The benefits of the exercise as well as the impact of such visualization activities on spatial orientation, particularly with respect to gender, are discussed. KEYWORDS: First-Year Undergraduate/General, Computer-Based Learning, Computational Chemistry, Lewis Structures, Molecular Modeling, VSEPR Theory

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INTRODUCTION With the continually growing field of computational chemistry, students and instructors have access to an ever-growing set of electronic resources to help explore and demonstrate concepts, such as molecular geometries, that may be difficult or abstract to many students. The classical ball-and-stick models can be traced back to Hofmann’s croquet ball models in 1865 and are still used as the major demonstration tool in general chemistry classes 150 years later.1 Although these types of models are useful in communicating geometry to another individual, students do not really get the benefit of trial and error in using these to develop their own understanding and chemical intuition when trying to determine the correct geometry for a given compound. The Valence Shell Electron Pair Repulsion, VSEPR, theory has recently celebrated 50 years in the field of chemistry.2−4 In order for students of general chemistry to use VSEPR theory to correctly predict the molecular geometry of a compound, students must first be able to correctly use Lewis Dot structures to find the number of electron lone pairs (LP) and sigma bonds (σ) around an atomic center. This sum of the LP and σ is called the steric number, or VSEPR number. Once students have correctly obtained the VSEPR number, only then can they begin to build a correct geometry according to VSEPR theory. It is easy to see that there are many places where students may find difficulty in arriving at the final geometry. Unfortunately, this concept is rarely taught with experimental data backing the “correct answer”. This kind of teaching does not help the student determine where they went wrong. © 2015 American Chemical Society and Division of Chemical Education, Inc.

The development of molecular modeling packages have allowed both the chemistry student as well as the practicing chemist to calculate optimized geometries of compounds with the implementation of many different theories ranging from ab initio to semiempirical to Newtonian force fields. Unfortunately, some of these theories fail to accurately predict experimental geometries and the learning curve for the use of these programs is often beyond the scope of the general chemistry student. Theoretical chemistry is a rapidly growing field of the chemical sciences. In mid-2008, U.S. News and World Report began including Theoretical as a chemistry specialty joining Organic, Inorganic, Physical, Analytical, and Biochemistry in their annual ranking of chemistry graduate programs.5 Molecular modeling and the use of theoretical models have a wide application in all areas of the chemical science. Introduction of the use and utility of these methods early in the chemistry curriculum will help increase the familiarity of these methods to students as well as easing the learning curve that often accompanies such computer-based modeling. In this paper, we present a unique approach to teaching Lewis Dot and VSEPR geometries using previously performed calculations of several structures to be analyzed in a variety of geometries. By providing students with calculation output files and some basic training on the graphical visualization program, students are able to use these calculated energies as the “pseudoexperimental” energy of the compound in a particular geometry. Predicted VSEPR geometries are then compared Published: July 30, 2015 1364

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with the “experimental” lowest energy structure as an experiment-driven verification of their VSEPR geometry structures.

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MATERIALS AND METHODS Gaussian 98 was used to calculate the energies of eight different structures each in 2−4 different geometries using the B3LYP/631G* level of theory.6 These structures were BCl3, CH4, CO2, CS2, NH3, NO2−1, PF5, and SF4. The geometry of each structure was restricted with respect to the corresponding bond angles in question and essentially forced each calculated structure to adopt a specific geometry (point group) while allowing each bond length to relax. Single point energy calculations of these final geometries were obtained and provided to the students. GaussView 5.0 was used to visualize and analyze each output file with regards to the calculated energy (Hartree−Fock, HF, unscaled and uncorrected) and the bond angles for each particular geometry presented.7 Energy differences (ΔHF) were converted to kcal/mol (1 hartree = 627.5095 kcal/mol). Students where then asked to compare their predicted geometry with the one that was shown to have the lowest calculated energy for each molecule.

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RESULTS AND DISCUSSION

Student Activity

The activity was presented to students in a General Chemistry I Laboratory section at Lamar University as a voluntary alternative to a regularly scheduled laboratory session. The entire activity was successfully completed in 2.5 h by all students following a 30 min lecture/demonstration of the software (3 h total laboratory time). Students were given an introductory lecture that included a demonstration of how to use GaussView 5.0 with respect to displaying the calculated energy and how to determine bond angles (Figure 1).

Figure 2. Example of completed student data sheet for the analysis of CH4.

4. Based on the Lewis structure, determine and list the VSEPR number (steric number) based on the number of electron lone pairs and sigma bonds around the central atom. 5. Based on the steric number and the number of electron lone pairs around the central atom, select the correct geometry (i.e., linear, tetrahedral, trigonal bipyrimidal) from the table provided (Table 1). 6. List the bond angle(s) based on the predicted geometry. 7. Draw the correct dash-wedge structure based on the information obtained.

Figure 1. Portions of the graphical interface student training for GaussView5.0.4

Obtain “Pseudoexperimental” from Molecular Modeling Calculations

1. Locate the output files for the molecule in question. File names begin with the molecular formula followed by a dash. Record the file name on the sheet. (i.e., ch4−1.log is the first methane geometry file.) 2. Open the file using the appropriate program for viewing (GausView5.0). 3. Rotate the molecule (click and drag) to view the molecule from various angles. 4. Determine the bond angles in the geometry provided by first selecting the “Bond Angle” icon and then selecting the three atoms of interest (making sure the central atom is the second one selected.) Record the observed bond angles.

Students were then given a written set of directions, the list of eight molecules to examine, 28 Gaussian output files, and worksheets where they were to record their results (Figure 2). The following is a brief summary of the directions that each student was given (complete details are provided in the Supporting Information). Lewis Dot and VSEPR Analysis

1. List the correct Lewis Dot structure of each atom in the compound. 2. Draw the Lewis structure based on the atoms drawn. 3. Redraw the structure by replacing shared electron pairs with solid lines. (No dash-wedge bonds yet) 1365

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Table 1. Molecular Geometries Based on VSEPR Structures

3. Exposure to Molecular Modeling software. “Pseudoexperimental” thermodynamic verification on why incorrect answers are not observed. 4. Opportunities to compare theory to “experiment” with the opportunity for re-evaluation of the student’s answers based on “actual results”. 5. Practice performing unit conversions (HF to kcal). To the best of our knowledge, the only other reported activity similar to the one proposed here was by Pfennig and Frock in 1999.8 They used advanced general chemistry students or upper level inorganic students working in groups of 3 or 4 over several weeks to construct the Lewis Dot structures, build the molecules within the computational software, and optimize the molecular geometries. Their approach presents several potential concerns that our exercise avoids. The difference in the lengths of time to complete the assignments (2 weeks vs 3 h) and the possible complications with inexperienced students performing geometry optimizations (i.e., local minima problem) are very noteworthy. Additionally, the inability of students to explore the calculated energies of possible “incorrect” (high energy) geometries limits the students’ learning whereas they have the opportunity to compare several energies in our method, which is a very valuable tool in molecular modeling. We have shown that the entire activity can be successfully completed by nonhonors first-semester general chemistry students independently within 3 h. Students get to compare the energies of different geometries as compared to a single optimized geometry, and by supplying the students with the output files; there is no need for students to wait for

5. Display and record the calculated energy of this structure as determined by the computation. (Results → Summary) 6. Repeat steps 1−5 for all calculated geometries of a given molecular formula. 7. Determine the geometry that has the lowest calculated energy and determine the relative energy (HF) that each molecule has in comparison to this lowest energy structure. (All relative energy numbers should be either zero or positive.) 8. Convert each relative energy from HF units to kcal/mol to determine how much higher in energy each structure is in comparison to the most stable, and therefore the observed “pseudoexperimentally” most stable structure (1 HF = 627.5095 kcal/mol). 9. Compare the geometry predicted using VSEPR theory to the calculated most stable geometry. If the predicted geometry is not the same as the calculated most stable geometry, reanalyze the Lewis dot and VSEPR process to find the possible source of the error and repeat the process. Benefits

Completion of the activity results in the following educational benefits: 1. Practice drawing Lewis Dot structures. 2. Demonstration in the connection between Lewis Dot and VSEPR theory. 1366

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Several studies exist that have examined the effects using 3-D models, including computer models, in developing the students’ skills in spatial reasoning and determining molecular structures.10−13 Moreover, development of spatial reasoning has been identified as a key skill set in many STEM disciplines, including chemistry.13 Therefore, implementing an activity that incorporates hands-on spatial reasoning experience in the first semester should help the development of these important skill sets. Research shows that development of spatial reasoning skills is not the same for male and female students and literature indicates that there is a significant gender gap in this area.12−14 We believe that implementation of activities such as the one reported here should help all students develop spatial reasoning skills and may assist in closing the gender gap by providing hands-on experience to all students, particularly females, in general chemistry courses.

calculations to be completed. Finally, we present students with additional experience performing unit conversions (HF to kcal), which helps to reinforce other topics within the general chemistry curriculum. Although students in higher level chemistry courses will have opportunities to compare experimental results with predicted VSEPR geometries (such as NMR chemical shifts or coupling constants), there exists very few opportunities like the one presented here for students of general chemistry. Faculty or upper-level students could examine experimental geometries obtained by experimental methods such as X-ray diffraction or theoretical methods such as geometry optimizations. Unfortunately, these examples still only supply the students with the answer of the geometry observed in nature and will not assist the student in understanding the flaw in their VSEPR analysis. When students discover that the other geometries are actually higher in energy, we believe that it will help understand the science beyond a set of rules in a text. Considering the increasing use of molecular modeling in the chemical sciences, it is important that students understand at an early stage that using theoretical calculations can be a very powerful tool for understanding and predicting chemical phenomena. Additionally, students will observe that many of the theoretical calculations result in geometries that will not be observed in nature and will not accurately describe the chemical behavior of the compounds, even though the calculations were successfully completed and still reported energies. By allowing the students to analyze output files of previously run calculations, students do not need to learn the details of the theoretical methods used or the construction of input files. Students are able to use the calculations as a tool to validate the “pencil-and-paper” techniques of Lewis dot and VSEPR theory. The experience and exposure to theoretical calculations in the first semester of general chemistry should be a valuable introduction to a technique that is gaining in popularity and utility throughout all areas of chemistry. The activity is also very cost-effective and easy to implement. Although this paper focuses on eight specific compounds, this activity could easily be expanded to include more examples, contracted to include fewer examples, or different structures could be used entirely. Each set of geometries needs to be calculated only one time and then can be distributed to the students. Therefore, there is no need for costly servers or for parallel computing, although recent options such as WebMO have made this aspect extremely convenient for educational purposes.9 For the implementation at our institution, we used a university purchased site license of GaussView5.0. This allows for the installation of the visualization software on any campus computers in any computer lab. Therefore, a single one-time investment has the potential application for thousands of general chemistry students. The use of Gaussian and GaussView was a personal preference of the authors; however the concept of using theoretical calculations to augment the student activity of using Lewis dot and VSEPR theory to determine molecular geometries can be implemented using other software packages as well. Graphical visualization software that includes the option show (or possibly toggle) the presence of electron lone pairs (orbitals or dummy-atoms) would be especially useful. If facilities and time permit, students may also be instructed on calculating the full energy minimized geometry on a few select structures. This additional aspect would also introduce the students to performing actual calculations to compare to their predicted geometries.

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CONCLUSIONS This paper describes a new and innovative activity for students in general chemistry that uses theoretical molecular modeling calculations in conjunction with Lewis dot and VSEPR theory to explore molecular geometries. Students use software to visualize the output files of compounds that were performed at various geometries. These output files are analyzed with regards to the geometries (bond angles) and relative stabilities (energies) of each compound in each particular geometrical configuration. Students are then able to use these data as “pseudoexperimental” observations in comparisons with their predicted VSEPR geometries. This activity provides students in the first semester of general chemistry with an exposure with molecular modeling software and allows students the opportunity to use computer models to improve their spatial ability, which has been shown to be a fundamental skill important in the sciences. Of particular benefit would be female students as this would help to close the gender gap that has been reported using spatial perceptual abilities.

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ASSOCIATED CONTENT

S Supporting Information *

The Supporting Information is available on the ACS Publications website at DOI: 10.1021/ed500806h. Full copies of the computational output files, student data sheets, lecture material, and student feedback (ZIP)

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AUTHOR INFORMATION

Corresponding Author

* E-mail: [email protected]. Notes

The authors declare no competing financial interest.

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ACKNOWLEDGMENTS The authors would like to thank the students who participated in this activity. Acknowledgment is made to the Lamar University Office of Sponsored Research for support (Gaussian/Gaussview). Partial support for this work was provided by the National Science Foundation’s Science, Technology, Engineering, and Mathematics Talent Expansion Program (STEP) under Award No. DUE-0757057. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do 1367

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not necessarily reflect the views of the National Science Foundation.

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REFERENCES

(1) McBride, J. M. Models and Structural Diagrams in the 1860s. https://webspace.yale.edu/chem125/125/history99/ 6Stereochemistry/models/models.html#Hofmann (accessed Sep 2014). (2) Gillespie, R. J.; Nyholm, R. S. Inorganic Stereochemistry. Q. Rev., Chem. Soc. 1957, 11, 339. (3) Gillespie, R. J. The electron-pair repulsion model for molecular geometry. J. Chem. Educ. 1970, 47, 18−23. (4) Gillespie, R. J. Fifty years of the VSEPR model. Coord. Chem. Rev. 2008, 252, 1315−1327. (5) U.S. News and World Reports. Best Chemistry Programs. http:// grad-schools.usnews.rankingsandreviews.com/best-graduate-schools/ top-science-schools/chemistry-rankings (accessed Sep 2014). (6) Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J. R.; Zakrzewski, V. G.; Montgomery, J. A.; Stratmann, R. E., Jr.; Burant, J. C.; Dapprich, S.; Millam, J. M.; Daniels, A. D.; Kudin, K. N.; Strain, M. C.; Farkas, O.; Tomasi, J.; Barone, V.; Cossi, M.; Cammi, R.; Mennucci, B.; Pomelli, C.; Adamo, C.; Clifford, S.; Ochterski, J.; Petersson, G. A.; Ayala, P. Y.; Cui, Q.; Morokuma, K.; Malick, D. K.; Rabuck, A. D.; Raghavachari, K.; Foresman, J. B.; Cioslowski, J.; Ortiz, J. V.; Baboul, A. G.; Stefanov, B. B.; Liu, G.; Liashenko, A.; Piskorz, P.; Komaromi, I.; Gomperts, R.; Martin, R. L.; Fox, D. J.; Keith, T.; Al-Laham, M. A.; Peng, C. Y.; Nanayakkara, A.; Gonzalez, C.; Challacombe, M.; Gill, P. M. W.; Johnson, B.; Chen, W.; Wong, M. W.; Andres, J. L.; Gonzalez, C.; Head-Gordon, M.; Replogle, E. S.; Pople, J. A. Gaussian 98, Revision A.7; Gaussian, Inc.: Pittsburgh, PA, 1998. (7) Dennington, R. D., II; Keith, T. A.; Millam, J. M. GaussView 5.0.9; Gaussian, Inc. : Pittsburgh, PA, 2008. (8) Pfennig, B. W.; Frock, R. L. The Use of Molecular Modeling and VSEPR Theory in the Undergraduate Curriculum to Predict the Three-Dimensional Structure of Molecules. J. Chem. Educ. 1999, 76 (7), 1018−1022. (9) WebMO − Computational Chemistry on the WWW. http:// www.webmo.net/ (accessed Sep 2014). (10) Springer, M. T. Improving Students’ Understanding of Molecular Structure through Broad-Based Use of Computer Models in the Undergraduate Organic Chemistry Lecture. J. Chem. Educ. 2014, 91, 1162−1168. (11) Kenney-Kennicutt, W. L.; Merchant, Z. H. Using Virtual Worlds in the General Chemistry Classroom. In Pedagogic Roles of Animations and Simulations in Chemistry Courses; Suits, J., Ed.; American Chemical Society: Washington, DC, 2013; pp 181−203. (12) Harle, M.; Towns, M. A Review of Spatial Ability Literature, Its Connection to Chemistry, and Implications for Instruction. J. Chem. Educ. 2011, 88 (3), 351−360. (13) Coleman, S. L.; Gotch, A. J. Spatial Perception Skills of Chemistry Students. J. Chem. Educ. 1998, 75 (2), 206−209. (14) Coluccia, E.; Louse, G. Gender differences in spatial orientation: A review. J. Environ. Psych. 2004, 24, 329−340.

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