In the Laboratory
W
Laboratory Sequence in Computational Methods for Introductory Chemistry Jason A. Cody* and Dawn C. Wiser Department of Chemistry, Lake Forest College, Lake Forest, IL 60045; *
[email protected] Over the last three years, we have designed, implemented, and evaluated a sequence of laboratory exercises that introduces first-year chemistry students to molecular modeling. The sequence expands upon students’ knowledge of bonding and VSEPR (valence shell electron pair repulsion) structures to build and submit semi-empirical calculations to MacSpartanPlus (1)1; uses the results to examine molecular shape, dipole moments, and intermolecular forces when coupled with a gas chromatography laboratory exercise; and finishes with an exploration of molecular orbitals. Earlier reports of computational exercises throughout the undergraduate curriculum (2–4) most often focus on upper-level physical and inorganic chemistry courses with “early” inclusion emphasizing the sophomore-level organic course (5–7). When these reports have involved first-year courses, the use of modeling software has been limited to viewing molecules and properties without incorporating the build-and-calculate stages required by the method (8) with only a few exceptions (9). Other reports compare physical and molecular properties, but do not involve a laboratory component (10). At Lake Forest College, the chemistry department’s laboratory curriculum emphasizes hands-on student use of research quality instruments and techniques. This sequence exposes first-year students to the predictive power of computational tools and to separation techniques and is followed by a two-week laboratory exercise in interpretation of proton FT-NMR spectra (11). This early exposure to modern instrumentation and computational chemistry is beneficial both for chemistry majors and for students whose exposure to chemistry is limited to the introductory course (12, 13).
pared to the observed retention times recorded on a gas chromatograph. The third exercise of the series includes distillation of a mixture of liquids and GC analysis of different fractions. Though not computational, this experiment builds upon the concepts realized in the previous computational exercises. Finally, the students calculate and view molecular orbitals of simple molecules. In all of the computational exercises, the student builds the molecules, submits the geometry and energy calculations, and interprets the results. Progression of the Laboratory Sequence Exercise 1: Molecular Shape and VSEPR Exercise 2: Molecular Dipole and Gas Chromatograph Retention Times Exercise 3: Distillation and Gas Chromatography Exercise 4: Molecular Orbitals 2
During Exercise 1 (Scheme I), structural details of four sets of molecules are carefully compared (Table 1). Students learn to generate molecular representations on the computer, to submit calculations, and to evaluate molecular structure and dipole moments. The ability to rotate the molecule on the computer screen in all directions increases the three-dimensional perception for the student. To reinforce this connection, we also have three-dimensional models of the molecules in the lab for manipulation. The students’ under-
draw Lewis structure from given chemical formula
Goals This four-week laboratory sequence spans both semesters of the first-year chemistry course and has been developed with the following pedagogical goals in mind: 1. Reinforce concepts of molecular shape, bonding, and polarity as they are introduced in class,
build molecule
2. Use computational results concurrently with experimental data to understand molecular properties,
submit geometry and surface calculation
3. Integrate complete hands-on use of modeling software including the build-and-calculate stages, 4. Reinforce good laboratory notebook practices, and 5. Emphasize continuity of course content and methods across semesters.
increase sophistication
display output
Sequence The laboratory sequence begins with a four-hour exploration of molecular shapes in which VSEPR predictions are compared to the molecular geometries obtained from semiempirical AM1 calculations. The following week, molecular dipole moments calculated by the modeling program are com-
record data, answer questions Scheme I. Diagram of the process for Exercise 1: Molecular Shape and VSEPR.
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In the Laboratory
standing of the graphical representations of the molecules is enhanced by questions that guide the study of the structures.W Theory and experiment are bridged in Exercise 2 (Scheme II). Students explore the intermolecular forces for the series of compounds given in Table 2 with the computer (Exercise 2a) and gas chromatograph (Exercise 2b). Notebook-keeping skills and skills learned in Exercise 1 are reinforced. New skills involve generation and interpretation of an electrostatic potential surface and use of a handbook to look up physical constants.4 Since the calculation time is short, ample time remains for the characterization of pure liquids and mixtures of liquids with the use of a gas chromatograph (HP5890 gas chromatograph equipped with a silicone microcolumn). For the computational portion of Exercise 2, the students look up the line formula and boiling point data for each compound, draw its Lewis structure, and calculate the dipole moment and electrostatic potential map. Carefully worded questionsW guide the interpretation of the electrostatic potential maps and dipole moments. Attention is given to the graphical and color output of the electrostatic potential so that the noted pitfalls may be avoided (14, 15). A data table containing this information is recorded in the notebook for later use. For the chromatography portion of Exercise 2, each student injects a pure liquid and a mixture of liquids into the GC using a needle-dip technique.5 Retention times on the GC are recorded and compared to the dipole moments calculated on the computer and to boiling point data (16). Although only one molecular property (boiling point) is examined in this exercise (17), the importance of hydrogen bonding as an intermolecular force is made very clear. The last compound eluted from the GC is not the one with the largest dipole moment! The students complete the first part (computation and handbook) of this experiment in the last laboratory session of the first semester and then finish the GC characterization portion during the first laboratory session of the second semester. Since there will be no opportunity for the students to repeat the calculations in the second semester once the GC portion is underway, the students are reminded to keep a careful notebook so that it may be used to complete the experiment. This split of one exercise into two parts emphasizes the importance of good laboratory notebook practices far better than any direction from an instructor.6 Exercise 3 (Scheme II) expands on the use of gas chromatography through the analysis of fractions from distillation.7 Knowledge gained by molecular modeling in the second week of the sequence aids in conceptual understanding of some of the forces involved in separations. In the final exercise (Scheme III) of the sequence, molecular modeling is used to calculate and view molecular orbitals (MOs). The essential components of MO theory are presented in the classroom portion of the course during the second week of the second semester. This approach separates the MO description of bonding from the valence bond (VB) theory that was introduced at the end of the first semester. MO theory is developed in class to the point where the nontrivial interaction diagram for carbon monoxide is given as homework. The concepts of highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) are introduced. The homework assignmentW asks 794
Table 1. Sets of Molecules Built, Minimized, and Analyzed in Exercise 1 Set
Molecules Built
Data Examined
1
CH3Cl, CH2Cl2, CHCl3
bond angles, bond length, dipole
2
PF5, SF4, ClF3
bond angles, molecular shape
3
C2H6, C2H4, C2H2
bond length
4
CH3CH2CH3, CH3OCH3, CH3CH2OH, CH3COCH3
complex structure, dipole
Table 2. Physical Constants for the Liquids Examined by Modeling and Gas Chromatography in Exercise 2 Compound fw (amu)
a
bp (°C)
a
µ (debye)b
Butanol
2-Butanone
Pentane
72.11
72.15
80
35
74.12 117.7 1.70
2.81
0.01
a
Data from ref 16.
b
See Note 3.
the students to predict the shape of the orbitals and to label them relative to the HOMO and LUMO (i.e., HOMO − 1, LUMO + 1, etc.) since that is how the calculations in MacSpartanPlus (1) are set up. In addition, the students must predict the type (π or σ) and bonding or antibonding character of the orbitals. Because a slightly higher level of theory8 is required for the calculation of the orbital shapes, the calculations take longer. Students notice the time difference, thus providing a perfect opportunity to point out that different levels of calculations are required for different objectives. After the calculations have been completed, the students examine the shapes of the molecular orbitals and compare the calculated results to the predictions they made as part of the prelaboratory assignment. Hazards There are no significant hazards in this laboratory sequence. However safety goggles should be worn when handling chemicals. Discussion A well-planned laboratory sequence integrating handson, student-centered experience with the cutting edge of chemical technology has tremendous impact on the student perceptions of the course. Several students have indicated on the course evaluations that they found the modeling exercises some of the most enjoyable and instructive of the semester. Each semester, a few students ask whether they can do some calculations on other molecules after the lab is finished! As the instructors, we have found that we are able to develop the students’ understanding of computational methods much farther in upper-level physical chemistry and inorganic chemistry classes. We are currently expanding our
Journal of Chemical Education • Vol. 80 No. 7 July 2003 • JChemEd.chem.wisc.edu
In the Laboratory
Exercise 2a: list of molecules, record physical data
new semester
Exercise 2b: GC characterization of liquids
Exercise 3: distillation and GC characterization semester ends
Prelab Assignment: interaction diagram
line formulas
Experiment
evaluate data, answer questions
Lewis structures
build molecules
calculate properties
build molecules
submit geometry and orbital calculations
compare to prelab exercise display output
Scheme III. Incorporation of prelaboratory homework assignment into the laboratory computer component of Exercise 4.
display output Computer
Scheme II. Progression for second and third laboratory experiments showing the relationship of computer and experiment.
computational offerings into the sophomore-level organic chemistry course as well (18). We observed that the students seldom confuse the two dominant bonding theories (VB and MO) since we have separated them in the course. Finally, we found that the students really understand the importance of notebook practices from the split in Experiment 2. Acknowledgments Financial support of this work from Lake Forest College is gratefully acknowledged. Some computer resources were obtained from Abbott Laboratories through their Resource Recovery Program. W
identify orbital type and symmetry
Supplemental Material
Notes for the instructor and detailed procedures, laboratory handout sheets, a prelaboratory homework assignment, and postexercise questions for the students are available in this issue of JCE Online. Notes 1. Any version of the Spartan software could be used. 2. In order to more closely follow some current introductory chemistry textbook sequences, Exercise 4 could immediately follow Exercise 1 since the required skills have been learned. 3. Dipole moments are calculated for the lowest-energy conformers in this table. 4. We have chosen to use the Aldrich catalog as an introductory handbook because it is easy to use and easily replaced. 5. The operator dips the needle into the solution to be sampled (liquid can be drawn up and evacuated if desired) and then inserts the “empty” needle into the instrument. The sample that sticks to the surface of the needle is sufficient for the experiment (more can swamp out the detector). 6. If students are new to the course in the second semester, the instructor or laboratory assistant helps them through the computational portion of the exercise.
7. A student-prepared mixture of cyclohexane and pentane (3:2) is distilled and analyzed. 8. An ab initio 3-21G(*) basis set is necessary to calculate the appropriate relative magnitudes of coefficients on contributing atomic orbitals (i.e., the lobes of the π and π* MOs are larger on the atom that has the nearest energy AOs).
Literature Cited 1. MacSpartanPlus, ver. 1.2.2, Wavefunction, Inc., 18401 Von Karman, Suite 370, Irvine, CA, 92612 also see http:// www.wavefun.com (accessed Apr 2003). 2. Pfennig, B. W.; Frock, R. L. J. Chem. Educ. 1999, 76, 1018– 1022. 3. Martin, N. H. J. Chem. Educ. 1998, 75, 241–243. 4. Gasyna, Z. L.; Rice, S. A. J. Chem. Educ. 1999, 76, 1023– 1029. 5. Hessley, R. K. J. Chem. Educ. 2000, 77, 203–205. 6. Kantardjieff, K. A.; Hardinger, S. A.; Van Willis, W. J. Chem. Educ. 1999, 76, 694–697. 7. Nelson, J. E.; Williamson, S. A.; Steffen, L. K. Chem. Educator 1996, 1, 1–9. 8. Wedvik, J. C.; McManaman, C.; Anderson, J. S.; Carroll, M. K. J. Chem. Educ. 1998, 75, 885–888. 9. Jones, M. B. J. Chem. Educ. 2001, 78, 867–868. 10. Laing, M. J. Chem. Educ. 2001, 78, 1544–1550. 11. Kateley, L. J. NMR Spectroscopy in the Introductory Laboratory; Presented at 30th Great Lakes Regional Meeting: Chicago, IL, May 1997. 12. Steehler, J. K. J. Chem. Educ. 1998, 75, 274–275. 13. Gillespie, R. J. J. Chem. Educ. 1997, 74, 484–485. 14. Shusterman, G. P.; Shusterman, A. J. J. Chem. Educ. 1997, 74, 771–776. 15. Shusterman, A. J.; Hoistad, L. M. Chem. Educator 2001, 6, 36–40. 16. Aldrich Handbook of Fine Chemicals and Laboratory Equipment 2000–2001 ed. Sigma-Aldrich, Inc.: Milwaukee, WI, 2000– 2001; 2907 pages. 17. Simpson, J. M.; Rivera, O. J. Chem. Educ. 2001, 78, 942– 943. 18. Martin, W. B.; Kateley, L. J.; Wiser, D. C.; Brummond, C. A. J. Chem. Educ. 2002, 79, 225–227.
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