In the Classroom edited by
Teaching with Technology
Gabriela C. Weaver Purdue University West Lafayette, IN 47907
Using the Cambridge Structural Database To Teach Molecular Geometry Concepts in Organic Chemistry Jay Wm. Wackerly, Philip A. Janowicz, Joshua A. Ritchey, Mary M. Caruso, and Erin L. Elliott Department of Chemistry, University of Illinois at Urbana–Champaign, Urbana, IL 61801 Jeffrey S. Moore* Departments of Chemistry, Materials Science and Engineering, and the Beckman Institute, University of Illinois at Urbana– Champaign, Urbana, IL 61801; *
[email protected] A large lecture classroom may not seem to give students a chance to move beyond their textbook structures and analyze data from actual molecular structures. However with continuous technological advances applied to education, individualized software programs are more commonly available to enhance students’ learning (1). It has been shown that students take a greater interest in their coursework when they have the opportunity to analyze “real-world” data (2). Given society’s growing dependence on information technology and the need to understand the basic concepts of data mining and parameter correlation, the opportunity to introduce these ideas in an organic chemistry classroom full of future professionals is appealing (3). Herein we share our progress on a set of two homework assignments that allows organic chemistry students to individually use the Cambridge Structural Database (CSD) to make structure correlations (4) that test students’ previously learned concepts of molecular geometry.
X d
C
R
C
C X = N or P
Figure 1. The generic structural motif used in the molecular geometry search query. The valence angles (θ) and distance out-of-plane (d ) were measured for each structure.
The CSD is a database of small organic and organometallic structures that have been elucidated by X-ray or neutron diffraction techniques (5). The database currently has 400,977 structures, and 43% of these are organic compounds. In order to give all of the students convenient access to the database, Classroom ConQuest was used.1 Classroom ConQuest is provided by the Cambridge Crystallographic Data Center free of charge2 although it contains a reduced number of structures (11,300). While only a subset of the full CSD, meaningful searches using Classroom ConQuest for simple structural trends can still be obtained. These assignments were designed to complement the lectures on molecular orbital theory in the Elementary Organic Chemistry II course at the University of Illinois at Urbana– Champaign. The course typically has an enrollment of 300–350 students, predominantly molecular and cell biology majors.3 In a class with very few chemistry majors, we feel it is important to incorporate assignments such as ours to stimulate students’ interest in the covered topics as well as introduce them to scientific technological advances. Each of the assignments and results are reported below, and the full assignments with answer keys are included in the online supplement. After the students have completed the database searches, imported their data into Excel, and answered questions to test their understanding of the assignment, the students turn in their work by uploading their completed assignments onto a Web based e-learning platform.4 To test long-term retention of information learned from these assignments, a survey was administered to a class.
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CŹPŹC CŹNŹC
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CŹNŹC Frequency
CŹPŹC Frequency
Molecular Geometry at Nitrogen and Phosphorus
Valence Angle / deg Figure 2. Histogram of the valence angles obtained from the CSD search of tricoordinate nitrogen and phosphorus.
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The first assignment was designed to investigate the geometry of nitrogen and phosphorus atoms in organic molecules that are acyclic and bonded to three carbon atoms.5 The CSD search results are set to provide the valence angles (θ) and distance out-of-plane (d ) (Figure 1). Using Classroom ConQuest, there are 151 hits in the database for nitrogen and 30 hits for phosphorus. A histogram of the valence angles for the resulting hits is shown in Figure 2. In general chemistry, students are taught the valence shell electron pair repulsion (VSEPR) model. This model predicts that atoms having three bonds and a lone pair will have a trigonal pyramidal geometry with a tetrahedral arrangement of the four electron pairs (6). If this model is valid, then all nitrogen
Journal of Chemical Education • Vol. 86 No. 4 April 2009 • www.JCE.DivCHED.org • © Division of Chemical Education
In the Classroom
Correlations of Bond Length, Twist, and Pyramidalization in N,N-Disubstituted Anilines The second assignment is designed for students to use a subset of data from the first assignment (all N,N-disubstituted anilines) and determine whether changes in the molecular geometry are correlated to propensity for n → π* orbital overlap (7). The students have learned in class that if substituents on the aniline nitrogen are twisted out of the plane of the benzene ring, the nitrogen lone pair is not aligned to the π-system for
π-type n → π* overlap. Conversely, they have been taught that when the substituents are in plane, the nitrogen lone pair is in the proper orientation for π-type overlap, resulting in a shorter aromatic C–N bond. The students test these conjectures by analyzing molecular geometries of structures in the CSD. The constraints are similar to the first assignment: the three C–N bonds must be acyclic and the N must be tricoordinate. The modifications to the CSD search are that two of the carbons must be tetracoordinate and the third carbon must be part of a phenyl ring, making an aniline structure. The search results are
Valence Angle / deg
and phosphorus atoms found in this search should be trigonal pyramidal with valence angles near 109.5°. If the angles were assumed to be 109.5°, a perfect tetrahedron, then the out-of-plane distances of nitrogen and phosphorus would be 0.48 Å and 0.61 Å, respectively (Figure 3). As Figure 2 shows, the data from the nitrogen structures indicate that only 32 of 152 data points fall in the range of 108–114°. Using the corresponding data points from Figure 3, the out-of-plane distances for the hits in this range are much larger than the remaining data points. When examining this set of narrow-angled nitrogen structures using the 3D Visualizer6 in ConQuest, it can be seen that they are trigonal pyramidal structures consistent with the VSEPR model. The majority of the data points for the nitrogen structures are at or near 120°. The structures with these wide angles and corresponding small out-of-plane distances (Figure 3) are more similar to trigonal planar molecules with sp2 hybridization, than to tetrahedral molecules with sp3 hybridization. When looking at many of these trigonal planar structures in the 3D Visualiser, students can see that the nitrogen is bound to at least one sp2 hybridized carbon (e.g., amides, anilines, etc.). Prior to undertaking this assignment, students were taught that the lone pairs of heteroatoms participate in π-type n → π* interactions. These data show that nitrogen is frequently in a geometry consistent with sp2-type hybridization, which contradicts the VSEPR model. From the scatter plot shown in Figure 3, the students see that there is a correlation between out-of-plane distance and valence angle. For nitrogen, the bond angles and out-of-plane distances change from an idealized trigonal pyramidal structure to an idealized trigonal planar structure with many structures lying in between. The correlation between these two structural parameters is not random but follows a parabolic trend. The nitrogen data in this trend is nearly continuous in the range of 109–120°. However, Figure 3 shows that the phosphorus data are found in a narrow range of out-of-plane distance and bond angles with an apparent linear trend between them. These data show that tricoordinate phosphorus atoms are always near the trigonal pyramidal geometry. The structure-correlation principle (4) correctly predicts that nitrogen inversion is a more facile process compared to phosphorus inversion because the angles along the inversion pathway are achieved by stable molecules for nitrogen but not for phosphorus. These data help to reinforce the concept that resonance overlap with an sp2 hybridized carbon is much less effective for phosphorus than it is for nitrogen. Additionally, this assignment allows students to see that although many structures do exist in the VSEPR-predicted geometries, the VSEPR model has shortcomings when describing certain classes of nitrogencontaining functional groups.
125 120 115 110 105 100
theoretical nitrogen theoretical phosphorous
C-N-C C-P-C
95 90 0.0
0.2
0.4
0.6
0.8
1.0
Out-of-Plane Distance / Å Figure 3. Scatter plot of valence angles versus out-of-plane distance of the N and P structures obtained from the CSD search. The open points indicate the bond distances for N and P assuming an ideal tetrahedral geometry.
N
dC-N U
C
C C
C
C N C
C
X1
C
C
N X2
C
C
Figure 4. The generic structural motif used in the aniline search query. The out-of-plane distance (d ), the aromatic, carbon-to-aniline nitrogen bond length (dC−N), and the two torsion angles (ω1 and ω2) were measured for each structure.
© Division of Chemical Education • www.JCE.DivCHED.org • Vol. 86 No. 4 April 2009 • Journal of Chemical Education
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required (90.2%). Most students agreed (rated 5–7 on a 7-point scale) that the assignments helped them understand the course material better (77.3%) and that the assignments’ objectives were clearly stated (90.3%). Students also found the assignments to be of moderate (3–5 on a 7-point scale) difficulty (69.0%). Time spent completing the assignments ranged widely, with the mode being 2–3 hours to complete both assignments (31.0%). The survey included six questions requiring students to interpret the concepts they learned from this assignment. All six questions had a multiple-choice component; two required an explanation to support the answer. The questions and the students’ responses are subsequently discussed. We note that students were given extra credit for completing the survey but not for the effort to do this; thus the reported percentages may be lower than what actually reflects the students’ knowledge. The first question displayed five structures obtained from the CSD search results in the first assignment (Figure 7). The students were asked to predict which conformation the specified nitrogen or phosphorus atoms would adopt. A slight majority (52.9%) of students, on average, were able to correctly predict the geometry. The most surprising result was that only 44% of the students correctly predicted that a structure containing phosphorus would have a trigonal pyramidal geometry, even though the results from the first assignment showed that all
CŹN Bond Length / Å
set to provide the out-of-plane distance (d ), the aromatic C to aniline N bond length (dC−N), and the two torsion angles (ω1 and ω2) (Figure 4). The average of the torsion angles ([ω1+ω2]/2) is defined as the twist angle. The twist angle describes the angular relationship between the nitrogen lone pair and the p orbitals of the benzene ring. Given these criteria, 44 structures are obtained. Figure 57 shows the relationship between the C–N bond length and twist angle with a parabolic trendline.8 Figure 6 7 relates outof-plane distance and twist angle with a parabolic trendline (7). The parabola maximum in Figure 5 correlates to the longest bond length and occurs at a twist angle of 93°, which is close to 90°, the largest twist angle possible, because angles of 0° and 180° indicate that the lone pair is in conjugation with the benzene ring. These data indicate that the longest aromatic C–N bonds correspond to an angle where the N lone pair is completely orthogonal to the orbitals of the aromatic ring. Conversely, the shortest bond lengths correlate to a twist angle with good orbital overlap between the N lone pair and the π system of the aryl group. The maximum of the parabola in Figure 6, which corresponds to the farthest out-of-plane distance, occurs at a twist angle of 92°. Again, this is close to 90°, implying that at the largest out-of-plane distances the nitrogen lone pair is orthogonal to the orbitals of the aromatic ring. Also, twist angles near 0° and 180° correspond to very short out-of-plane distances indicating that at these angles, the N lone pair is nearly parallel with the orbitals of the benzene ring. From these two graphs, students can conclude that their conjectures about geometric correlations are consistent with experimental results. If the lone pair is 90° away from the orbitals of the aromatic ring then no conjugation exists, the nitrogen is pyramidal, and the nitrogen-aromatic ring carbon bond is consistent with the length of a C–N single bond (8). Furthermore, students can see that there are not just two states, conjugated or not conjugated, but that many structures lie at twist angles other than 0°, 90°, or 180°. These structures with intermediate twist angles follow a parabolic trend with respect to both the nitrogenaromatic carbon bond length and out-of-plane distance.
1.47 1.44 1.41
ź
y ä (ź1.16 ò 10 5)x2 ź á (2.18 ò 10 3)x + 1.35
1.38 1.35
R2 ä 0.635
1.32 0
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Figure 5. Scatter plot of the aromatic C–N bond length versus twist angle of the N structures obtained from the CSD search. The best-fit line and corresponding equation is a second-order polynomial.
Out-of-Plane Distance / Å
At the conclusion of the assignment, a survey was administered to students via a Web-based, e-learning platform during the spring semester of 2007.9 Students were not informed of the survey contents and were asked not to discuss the survey with other students or refer to their notes. The survey was administered roughly two months after the due-date of the first assignment and roughly one month after the due-date of the second assignment in an effort to test the students’ long-term memory. In addition to testing the students’ retention of the information, we obtained demographic information and deduced the strengths and weaknesses of the assignments. Most students (87.8%) enrolled in the course completed the survey, making the survey results representative of the entire class. Of the 287 students who completed the survey, a majority were females (56%), life science majors (63.1%), second-year students (60.3%), and persons aged 19–20 (70.4%). A majority earned an A or B letter grade in the preceding organic chemistry course (70.7%) and expected to earn an A or B letter grade in the present organic chemistry course for which these assignments are
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Twist Angle / deg
Survey
0.5 0.4
ź
0.3
y ä (ź5.56 ò 10 5)x2 ź á (1.02 ò 10 2)x ź3 ź 8.29 ò 10
0.2 0.1
R2 ä 0.916
0.0 0
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Twist Angle / deg Figure 6. Scatter plot of out-of-plane distance versus twist angle of the N structures obtained from the CSD search. The best-fit line and corresponding equation is a second-order polynomial.
Journal of Chemical Education • Vol. 86 No. 4 April 2009 • www.JCE.DivCHED.org • © Division of Chemical Education
In the Classroom
of the phosphorus atoms had a trigonal pyramidal geometry. These results indicate that a little more than half of the time the students could identify the preferred geometries for nitrogen and phosphorus atoms. In the second survey question, a histogram was presented showing the results obtained from a CSD search similar to first assignment, only arsenic was put in place of nitrogen or phosphorus (Figure 8). The students were then asked to interpret the histogram and predict the molecular geometry of arsenic. Over two-thirds of the students (68.3%) were able to identify trigonal pyramidal as the correct geometry. This result showed that most of the students were able to interpret the geometries of molecules based on looking at a histogram of valence angles. For the third survey question, a CSD search similar to that of the first assignment was performed except that the carbons were constrained have a coordination number of four. The students were then asked to choose the histogram of C−N−C valence angles that they would expect to result from this search.
Cl
Cl
Ph
N
P S Me Me3Si
Cl
Me3Si
O EtO NH
N
SiMe3 SiMe3 SiMe3
Cl
NO2
OEt Me
Me
Me
Me3Si O
Me
N
Ph
OEt
N Me
O
Cl
Figure 7. Five structures obtained during the CSD search from the first assignment. In the survey, the students were asked to predict which conformation the atoms shown in bold would adopt.
25
Frequency
20 15
About half of the students (48.8%) were able to correctly identify the histogram which gave values corresponding to a more pyramidal nitrogen. The second most frequently chosen response (23.7%) was the same histogram obtained by the students from the nitrogen search of the first assignment. The fourth question of the survey came directly from the set of questions required by the first assignment. The survey question asks whether the rate of inversion for pyramidal nitrogen or phosphorus is faster. More than three-quarters of the students (77.4%) answered the question correctly, which indicates they could recall the correct answer from the assignment. When the students were asked to explain their answer, the results indicated that most of the students (66.2%) did not understand or misinterpreted the question. We believe that no meaningful data can be drawn from this free response question. The final two survey questions were considered to be the most difficult because they required interpretation and a good memory of the assignment. The fifth survey question asked the students, based on what they learned from the second assignment, whether they would expect a correlation between C−N bond length and out-of-plane N distance for disubstituted anilines. If the student believed a correlation existed, then they were asked what type of correlation they would predict. We were pleased to see that over one-third of the students (34.8%) correctly expected there to be a linear correlation between the two. Conversely, the most frequently chosen distractor (52.6%) stated that the correlation would be parabolic, which is the same trend that was seen in the second assignment for the C−N bond length versus twist angle (Figure 5) and the out-of-plane distance versus twist angle (Figure 6). In the sixth survey question, the students were shown the phosphorus data from the first assignment (Figure 3) without the nitrogen data present and with the slope, y intercept, R2 values, and a linear trendline drawn through the data.10 The students were then asked whether it is reasonable to assume that if similar phosphorus molecules exist with smaller out-of-plane distances would they expect the linear trend to continue. Many more students expected the trend to continue (59.6%) than did not (28.9%). We predicted that this would be the case because these assignments were designed to teach students about trends in molecular geometry; however, we wanted to see which of the students could make the conceptual leap to realize that a y-intercept value of 132 would mean 132° bond angles around phosphorus if the out-of-plane distance were 0. Since this would be impossible the trend could not continue.11 To probe whether the students were able to understand why the trend could not continue, we asked the students to explain their answer to this question. We identified that 15% of the students were able to show some level of understanding of this concept. Conclusions
10 5 0 90
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Valence Angle / deg Figure 8. Histogram of the valence angles obtained from a CSD search of tricoordinate arsenic.
We have described a set of two homework assignments currently used in our organic chemistry course. They were designed with two goals: the first was to help second-semester organic chemistry students better understand simple orbital concepts and the relationship to molecular geometry and the second was to give students the opportunity to use technology (the CSD and ConQuest visualizer) to observe the structures of
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experimentally determined crystal structures. Additionally, these assignments asked the students to challenge models learned previously in their chemistry courses. In one case, they found data contrasting what is usually learned in general chemistry courses. The survey administered to the most recent class showed a moderate amount of long term retention by the students. We also discovered that some students were able to integrate what they learned and apply these concepts to new problems. However, we feel that some aspects of this assignment could be improved to help students retain the concepts instead of simply remembering the answers from the assignments. We encourage comments or suggestions for improvement of these assignments and have included the online supplement with the assignments for any organic chemistry educators to use in their classrooms. Acknowledgments The authors would like to thank the University of Illinois Chemistry Learning Center, Patricia Phillips-Batoma, and Jerome Baudry. Their initial and continual assistance made these assignments possible. Notes 1. Students are given the option of installing a copy of Classroom ConQuest on their own computers or using a computer provided for them by a departmental computing facility. 2. This is provided free with a full CSD license. 3. Chemistry and chemical engineering majors usually take a different course at the University of Illinois. 4. Using an online platform the assignments can be either graded automatically or individually by an instructor or TA. Currently we grade the first assignment individually and the second one automatically. 5. See the online supplement for full details for how the structure searches were performed. 6. 3D Visualiser is a chemical visualization program that allows students to look at a pseudo-three-dimensional image of the molecule because they can rotate, move, and zoom in on the structure shown on the computer screen in one of many different models (e.g., ball and stick, space filling, etc.). 7. Even though the twist angle could be reported on a scale of 0–90°, we show the angles going from 0–180° because these are the data obtained directly by the ConQuest program. We leave the data the way they were obtained for simplicity of analysis by students. 8. One of the data points has been removed because it is a significant outlier. The students are introduced to the concept of statistical outliers in data analysis. See the aniline assignment in the online supplement for more details. 9. The survey was administered at this time because it was the most recent semester before this manuscript was submitted.
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10. See the survey results in the online supplement for more details. 11. A full CSD search was performed that does show the phosphorus data starting to significantly deviate from the linear trend at smaller out-of-plane distances.
Literature Cited 1. (a) Smith, S.; Stovall, I. J. Chem. Educ. 1996, 73, 911–915. (b) Ram, R. R.; Ciochina, R.; Grossman, R. B.; Finkel, R. A.; Kannan, S.; Ramachandran, P. J. Chem. Educ. 2006, 83, 164–169. (c) Cole, R. S.; Todd, J. B. J. Chem. Educ. 2003, 80, 1338–1343. (d) Freasier, B.; Collins, G.; Newitt, P. J. Chem. Educ. 2003, 80, 1344–1347. (e) Hall, R. W.; Butler, G. L.; McGuire, S. Y.; McGlynn, S. P.; Lyon, G. L.; Reese, R. L.; Limbach, P. A. J. Chem. Educ. 2001, 78, 1704–1708. (f ) Penn, J. H.; Nedeff, V. M.; Gozdzik, G. J. Chem. Educ. 2000, 77, 227–231. 2. (a) DeHaan, R. L. J. Sci. Educ. Technol. 2005, 14, 253–269. (b) Prince, M. J. Eng. Educ. 2004, 89, 1–9. (c) Handelsman, J.; EbertMay, D.; Beichner, R.; Burns, P.; Chang, A.; DeHaan, R.; Gentile, J.; Lauffer, S.; Stewart, J.; Tilghman, S. M.; Wood, W. B. Science 2004, 304, 521–522. 3. (a) Davis, T. V.; Zaveer, M. S.; Zimmer, M. J. Chem. Educ. 2002, 79, 1278–1280. (b) Guterman, L. Chronicle Higher Educ. 2001, 47, A14. 4. Bürgi, H. B.; Dunitz, J. D. Acc. Chem. Res. 1983, 16, 153– 161. 5. (a) Allen, F. H. Acta Crystallogr. 2002, B58, 380–388. (b) Bruno, I. J.; Cole, J. C.; Edgington, P. R.; Kessler, M.; Macrae, C. F.; McCabe, P.; Pearson J.; Taylor, R. Acta Crystallogr. 2002, B58, 389–397. 6. Gillespie, R. J.; Popelier, P. L. A. Chemical Bonding and Molecular Geometry; Oxford University: New York, NY, 2001; pp 94–98. 7. This assignment is based on the article by Gilli, G.; Bertolasi, V.; Bellucci, F.; Ferretti, V. J. Am. Chem. Soc. 1986, 108, 2420– 2424. 8. Zumdahl, S. S. Chemistry, 4th ed.; Houghton Mifflin: Boston, MA, 1997; p 368.
Supporting JCE Online Material
http://www.jce.divched.org/Journal/Issues/2009/Apr/abs460.html Abstract and keywords Full text (PDF) Links to cited URLs and JCE articles Supplement Assignments 2 and 3 with answer key for instructors
Survey instrument on the Cambridge Structural Database assignments with students’ response data
Journal of Chemical Education • Vol. 86 No. 4 April 2009 • www.JCE.DivCHED.org • © Division of Chemical Education
