LABORATORY EXPERIMENT pubs.acs.org/jchemeduc
Looking Beyond Lewis Structures: A General Chemistry Molecular Modeling Experiment Focusing on Physical Properties and Geometry Kimberly J. Linenberger,† Renee S. Cole, and Somnath Sarkar* Department of Biochemistry, Chemistry and Physics, University of Central Missouri, Warrensburg, Missouri 64093, United States
bS Supporting Information ABSTRACT: We present a guided-inquiry experiment using Spartan Student Version, ready to be adapted and implemented into a general chemistry laboratory course. The experiment provides students an experience with Spartan Molecular Modeling software while discovering the relationships between the structure and properties of molecules. Topics discussed within the experiment include dipole moments, bond angles, bond lengths, selected periodic properties, resonance structures, electron density potential maps, and molecular shapes. KEYWORDS: First-Year Undergraduate/General, Laboratory Instruction, Physical Chemistry, Inquiry-Based/Discovery Learning, Lewis Structures, Molecular Modeling, Molecular Properties/Structure, Resonance Theory, Student-Centered Learning, VSEPR Theory
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isualization of models and making rational conclusions based on observations are critical skills needed by chemists. Chemists apply these skills in many instances, such as when studying the structure of biomolecules for drug design or understanding crystal structures of materials for product development.1 Molecular modeling and computation have become viable educational and research tools as computers and programs have increased in processing capabilities and affordability. This makes it possible to help students develop these critically needed visualization skills by introducing students to computer modeling and computation. This article describes a general chemistry laboratory experiment that utilizes the molecular modeling software, Spartan Student Version,2 to help students understand the relationships between structures (both electronic and molecular) and properties of molecules commonly discussed in introductory chemistry such as dipole moments, bond angles, bond lengths, selected periodic properties, and molecular shapes. In addition, the experiment focuses on developing the concept of resonance structure and resonance hybrid in a unique manner through the use of sulfuric acid, bisulfate ion, and sulfate ion. The modification of the experiment from a Lewis structure-molecule building verification experiment to its present form is discussed to show how the experiment in the present form evolved. This laboratory was developed as part of a National Science Foundation Course, Curriculum, and Laboratory Improvement (NSF-CCLI) Program grant to equip a computer laboratory to support integration of visualization and computation into the curriculum. Similar curriculum enhancement projects have been reported in this Journal;36 however, there has been little dissemination of the actual experiments as a means to further the advancement of undergraduate curricula at other institutions. There are multiple experiments in this Journal313 that expose undergraduates to molecular modeling and computer calculations, but only a few focus on introductory or general chemistry courses.6,7 Of these few general chemistry experiments, only Cody and Wiser7 provide an actual written experiment for immediate use in the reader’s institution. Copyright r 2011 American Chemical Society and Division of Chemical Education, Inc.
This experiment was developed based on tested pedagogy that bridges the domains of research and practice. The experiment is based on the learning cycle (data collection, concept invention, and application), a constructivist framework, and follows a guided-inquiry design in which students are led through the process of hypothesis formation and testing via embedded questions, to make connections between observations and principles.14 The laboratory inquiry rubric15 was used to gauge to what extent this experiment could be deemed inquiry and falls within a level 1 use of inquiry. This level describes an experiment in which the question and procedures are given to the student but the student must interpret the results. Fay et al. tested the rubric with several commercially available laboratory programs and found that self-described guidedinquiry experiments15 were reliably rated a level 1. This rating is consistent with the rating of the experiment set forth in this article.
’ DEVELOPMENT The original intention of the authors was to use three-dimensional visualization to enhance the traditional Lewis structure lab that was included in our laboratory curriculum in which students drew structures and built hand-held models using model kits. After the initial implementation, it was realized that there were few learning gains over our traditional lab and we were not using the power of the molecular modeling software to truly enhance the student learning experience. We wanted to use the technology to improve students’ understanding of structure and properties at a level that is difficult to accomplish using paper and pencil or fixed hand-held models. We also wanted students to understand the limitations of the models used to represent molecules (Lewis structures) and theoretical models (valence-shell electron pair repulsion: VSEPR) in understanding structure. VSEPR is an empirical construct that is simplistic and works well in developing Published: April 19, 2011 962
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Table 1. Concepts, Structures, and Data For Each Laboratory Period Class Period 1
Concept
Structure
Data
Bond Order
C2H6, C2H4, C2H2, F2, O2, N2
Bond distance
Atomic Size
Cl2, I2, ICl
Bond distance
Resonance Structure, Resonance Hybrid
CH4, NH3, H2O
Bond angle
H2SO4, HSO4, SO42-
Bond distance Bond angle Dipole moment Electron density potential map
2
Valence-Shell Electron Pair Repulsion (VSEPR) Theory
CF4
Energy Bond distance
NH4þ, NH3, NH2
Bond angle Dipole moment Electron density potential map
SO3, CO32-
Valence-Shell Electron Pair Repulsion (VSEPR) Theory, Electronic and Molecular Geometry
Bond distance
CH4, NH3, H2O
Bond angle
ClF3, SF4, SOF4
Dipole moment
SF6, BrF5
Electron Density Potential MAP Energy value and energy minimization
NO2, CO2, SO2, COS
Valence-Shell Electron Pair Repulsion (VSEPR) Theory, Electronic and Molecular Geometry, Odd electron molecule
Bond distance Bond angle Dipole moment
qualitative understanding of the structures of molecules and ions. A thorough review of VSEPR theory can be found in the Journal articles by Gillespie.16,17 We wanted to bridge the VSEPR model with higher-level theories that are based on quantum mechanics without requiring an in-depth knowledge of quantum mechanical principles. Even though students are using quantum mechanical methods to calculate structure, we are solely having the students use pattern recognition and comparison. Therefore, understanding of the principles of quantum mechanics is not necessary to accomplish the learning goals.
not to analyze the methods, but to use the method to help students analyze trends and patterns. Students are required to complete a pre-laboratory assignment before each lab period that involves drawing the Lewis structures for the molecules and ions under consideration. In addition, students answer a few questions related to the topic under investigation so that they can test their predictions and make successful connections between data and principles. At the beginning of the laboratory, students check the accuracy of their Lewis structures by comparing their structures with the correct structure stored in our server. Once they have checked their structures, students build and optimize the geometry of the molecules and ions in Spartan Student Version as prompted in the laboratory manual. Students then use necessary visualization tools and gather data to answer questions and make inferences. Table 1 lists the molecules and ions used to illustrate each concept addressed during each lab session and identifies the data students collect in each instance. The first period begins with students using the molecules C2H6, C2H4, C2H2, F2, O2 and N2 to determine the trend of bond length in accordance with bond order and atomic size. The intent of this section is for students to understand that bond lengths are affected by both the atomic size and bond orders. However, depending on the specific situation, one of these parameters may play a more dominant role in predicting trends in bond lengths. Students perform geometry optimization, determine the bond length for Cl2 and I2, and then use this information to predict the bond length of ICl. Geometry optimization and determination of bond length of ICl help them test their hypothesis and check the validity of the reasoning behind their prediction. The first period concludes with an exploration of the concept of resonance structures and the resonance hybrid. Students perform geometry optimization on sulfuric acid, one of the resonance structures of hydrogen sulfate, and of the sulfate anion. Students gather data on bond lengths, bond angles, and
’ EXPERIMENT The experiment is designed to be completed in two 3-h laboratory periods and is divided into concept areas appropriate for the time allotments. The only prerequisite knowledge required is a familiarity with periodic trends in atomic size and electronegativity as well as an ability to draw Lewis structures. This laboratory should be implemented at the time that students are introduced to drawing Lewis structures, but preferably before resonance and molecular shape are discussed in detail. The rationale behind this suggested sequence is to use the graded student reports as a formative assessment item to address a variety of student misconceptions associated with structures and electronic properties of molecules and ions. All computational calculations were done using the 6-31G* ab initio method (unless otherwise noted) using Spartan Student Version. Any molecular modeling software is applicable to conduct this laboratory as long as it has the ability to calculate equilibrium geometry, dipole moments, and electron density potential maps for the given molecules and ions. The calculated values of structural parameters and physical properties are not compared with experimental values known from crystal structures or spectroscopic data because the intent of the laboratory is 963
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Journal of Chemical Education dipole moments for each species and then use the electron density potential maps to gauge the electron density distribution on oxygen atoms. Students answer several questions on resonance structures based on the collected data with the intent that they realize the underlying empirical nature of resonance structures and the limitations of Lewis structures in representing the actual resonance hybrid. The second period is focused on the relationships between electronic geometry and molecular shapes. Students perform geometry optimization on several simple molecules, the shapes of which are commonly covered in general chemistry. Students use the data collected for the various molecules and ions to determine the electronic and molecular geometry of each species. In this process students uncover the VSEPR theory by creating the table of geometries commonly found in general chemistry textbooks. Therefore, this is a unique guided-inquiry approach in which students determine various shapes and learn how geometric shapes affect molecular polarity and electron density on atoms. Students begin the second period by comparing the energies of CF4 as a square-planar (structure similar to how students typically draw the Lewis structure) and a tetrahedral structure. Students then use the data to infer that a tetrahedral structure is more stable and therefore is the preferred geometry of the CF4 molecule over a square-planar geometry. By comparing corresponding angles and the energy of several structures (see Table 1), students discover how the atoms in a molecule are oriented in space to reach the lowest possible energy. Students fill out their table of electronic and molecular geometries using the data collected as they make inferences from their data. Finally, at the end of the second period, students are asked to apply their broader understanding of structure and properties gained by this laboratory experience. The key feature of this approach is that students are collecting data similar to that on which the VSEPR theory is based. Students are then analyzing and interpreting that data for themselves in order to arrive at the tenets of the VSEPR theory on their own.
’ IMPLEMENTATION All laboratory sections complete the same laboratory exercises each week. The laboratory exercise described here is completed in a computer classroom with 32 student computers and one instructor computer station, which is connected to a projector. Spartan Student Version is installed on all of the computers in the classroom, and the instructor has the ability to demonstrate the use of Spartan or answer global questions. The design of the facility is such that a pair of students can be seated at each computer. The lab is generally conducted with 2458 students in the computer laboratory, depending on whether one or two laboratory sections are meeting at a given time. If two sections are meeting concurrently, both instructors are in the classroom to facilitate the laboratory activity. Students work in pairs to complete the activity even when there are enough computers for each student. It is essential that students have a strong foundation in drawing Lewis structures to build appropriate structures in Spartan. This laboratory is designed to be a guided-inquiry investigation of molecular structure, shape, and function in relationship to molecular properties. Therefore, students should be given ample opportunity to inquire. Instructors may want to follow up with class discussions of results after each section and as necessary during the investigation if and when surprising data emerges for
LABORATORY EXPERIMENT
the results. Instead of the instructor telling students the difference in bond angles for methane, ammonia, and water (referring to literature values), students make predictions based on their prior understanding and generate data that has to be explained. This is consistent with constructivist theories of learning.
’ TYPICAL STUDENT RESULTS The general chemistry laboratory at our institution is an integral part of the lecture course and a grade is assigned for the course. The laboratory component is counted as a certain percent of the total points assigned to the overall course grade. Each lab for general chemistry counts toward the total points assigned for the laboratory component. Students in this lab obtain a certain portion of the allocated points for performing the experiment and collecting the data. Additional points are allocated for questions that require student to make predictions, analyze data, or make inferences. These questions are indicated with an asterisk in the instructor’s notes in the section, “solutions to questions”, in the Supporting Information. Specific points are allocated for each of these questions depending on the extent to which students are meeting the objectives of the laboratory activity. Analysis of the lab reports provides evidence that the majority of students meet four of the six objectives. Students are able to use the program to build and view the designated molecules and ions to collect the required data (objective i). Students are able to predict and analyze relationships between bond types and bond strength (objective ii) and typically can articulate how periodic trends relate to structural characteristics (objective iii). Students are most successful in determining the molecular geometry of molecules (objective iv), with more than 90% of students able to describe all the shapes as well as being able to calculate structures and answer questions in the applications and extensions section. The two objectives for which more students are still progressing are in understanding the concept of resonance structures (objective v) and interpreting electron density plots (objective vi). In these two areas, student written responses indicate a lack of clarity in their understanding and a limited use of scientific vocabulary. By completing the laboratory exercise before the concepts are discussed in depth in the lecture portion of the course, the laboratory can serve as a formative assessment. The instructor can then address student misconceptions and incomplete understandings in the lecture. Students also perceive a benefit to completing the laboratory. When asked, by free-response survey, if this activity helped to visualize and extract information from the molecular structures, 82% of the students assessed said yes it helped them understand molecular structures at a deeper level. Some of the ways in which the students mentioned it helped include (i) seeing the 3D structure versus the paper pencil sketch and (ii) seeing the structures and shape geometry and relating them to electronic properties. ’ HAZARDS There are no hazards associated with this laboratory beyond those that accompany sitting in front of a computer. ’ CONCLUSION This laboratory is designed to help students understand the relationship between structure and properties of molecules 964
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commonly discussed in introductory chemistry. The structure of molecules and properties are generally covered in an isolated fashion in most curricula. This laboratory combines the understanding of structure (both electronic and molecular) and properties of several molecules and ions and addresses some critical concepts such as resonance, dipole moments, selected periodic properties, and molecular shapes. It is suitable for an introductory general chemistry course because it takes a guidedinquiry approach in which students explore structureproperty relationships in depth by doing analysis of computational data. It also provides an opportunity for students to develop a more scientifically appropriate vocabulary and ability to visualize and describe molecular models.
’ ASSOCIATED CONTENT
bS
Supporting Information Notes for the instructor and detailed procedures; laboratory handout sheets; a prelaboratory homework assignment; and answers to the laboratory questions. This material is available via the Internet at http://pubs.acs.org.
’ AUTHOR INFORMATION Corresponding Author
*E-mail:
[email protected]. Present Addresses †
Department of Chemistry and Biochemistry, Miami University, Miami, Ohio 45056, United States.
’ ACKNOWLEDGMENT We wish to thank the National Science Foundation for support of this project (NSF DUE#0411104). We also wish to thank the students and instructors who have provided valuable feedback in the development of this laboratory exercise. In particular we would like to thank Gwen Giffin and Courtney Bloodgood. ’ REFERENCES (1) Truhlar, D. G.; McKoy, V. Comput. Sci. Eng. 2000, 2, 19–21. (2) Spartan, Wavefunction, Inc. Home Page, Irvine, CA. http:// www.wavefun.com (accessed Apr 2011). (3) Paselk, R. A.; Zoellner, R. W. J. Chem. Educ. 2002, 79, 1192–1194. (4) Martin, N. H. J. Chem. Educ. 1998, 75, 241–243. (5) Jones, M. B. J. Chem. Educ. 2001, 78, 867–868. (6) Feller, S. C.; Dallinger, R. F.; McKinney, P. C. J. Chem. Educ. 2004, 81, 284–287. (7) Cody, J. A.; Wiser, D. C. J. Chem. Educ. 2003, 80, 793–795. (8) Pfennig, B. W.; Frock, R. L. J. Chem. Educ. 1999, 76, 1018–1022. (9) Gasyna, Z. L.; Rice, S. A. J. Chem. Educ. 1999, 76, 1023–1029. (10) Hessley, R. K. J. Chem. Educ. 2000, 77, 203–205. (11) Kantardjieff, K. A.; Hardinger, S. A.; Van Willis, W. J. Chem. Educ. 1999, 76, 694–697. (12) Clauss, A. D.; Nelson, S. F. J. Chem. Educ. 2009, 86, 955–958. (13) Chadroff, L. C.; O’Neal, T. M.; Long, D. A.; Hemkin, S. J. Chem. Educ. 2009, 86, 1072–1076. (14) Farrell, J. J.; Moog, R. S.; Spencer, J. N. J. Chem. Educ. 1999, 76, 570–574. (15) Fay, M. E.; Chem. Educ. Res. Prac. 2007, 8, 212–219. (16) Gillespie, R. J. J. Chem. Educ. 1992, 69, 116–121. (17) Gillespie, R. J. J. Chem. Educ. 2004, 81, 298–304. 965
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