Teaching Three-Dimensional Structural Chemistry Using Crystal

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Teaching Three-Dimensional Structural Chemistry Using Crystal Structure Databases. 4. Examples of Discovery-Based Learning Using the Complete Cambridge Structural Database Gary M. Battle,*,† Frank H. Allen,† and Gregory M. Ferrence‡ † ‡

Cambridge Crystallographic Data Centre (CCDC), 12 Union Road, Cambridge CB2 1EZ, United Kingdom Department of Chemistry, Illinois State University, Normal, Illinois 61790-4160, United States ABSTRACT: Parts 1 and 2 of this series described the educational value of experimental three-dimensional (3D) chemical structures determined by X-ray crystallography and retrieved from the crystallographic databases. In part 1, we described the information content of the Cambridge Structural Database (CSD) and discussed a representative teaching subset of ca. 500 CSD structures that have been selected for their educational relevance. In part 2, we exemplified the value of the CSD teaching subset by describing four worked examples of their use in a teaching context. Although the CSD teaching subset and its associated learning modules provide a major resource for chemical educators, there are many cases where the full CSD System is essential to make an educational point. In part 3, we describe the complete CSD System and its associated software and highlight the extended range of discovery-based learning opportunities this affords. Here, we illustrate a number of teaching examples that take advantage of the massive structural information content of the complete CSD System to broaden and enhance the chemical education experience, including, for example, studies of mean molecular dimensions, stereochemistry and conformations, metal coordination sphere geometries, hydrogen bonding and other supramolecular phenomena, and reaction pathways. KEYWORDS: First-Year Undergraduate/General, Graduate Education/Research, Second-Year Undergraduate, Upper-Division Undergraduate, Chemoinformatics, Computer-Based Learning, Inquiry-Based/Discovery Learning, Internet/Web-Based Learning, X-ray Crystallography

arts 1 and 2 of this series1,2 described the value of crystal structure information in teaching fundamental concepts in three-dimensional (3D) structural chemistry. These articles introduced the Cambridge Structural Database (CSD)3a and Web-based software tools and showed how a Web-accessible teaching subset of some 500 CSD entries could be used to exemplify and study the 3D aspects of, for example, aromaticity, ring conformations, stereochemistry and chirality, hapticity, and VSEPR theory. Although the CSD teaching subset and its associated learning modules provide a major resource for chemical educators, there are many cases where the full CSD System, now covering more than 500,000 crystal structures, is essential to make an educational point. This is particularly true when introducing students to variance in real experimental observations, for example, where many hundreds of observations are required to generate statistically meaningful trends from the structural data or simply introducing students to the search and manipulation of data that

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Copyright r 2011 American Chemical Society and Division of Chemical Education, Inc.

are commonly available in large chemical and biochemical databases. Therefore in part 3,4 we described the full CSD System, that is, the complete CSD database of more than half a million crystal structures, and a more extensive set of software tools: ConQuest for database searching, Mercury for structure visualization, and Vista for data analysis. Detailed information about accessing the full CSD System was also provided. We illustrated the use of this software for enhancing the chemical learning experience through studies of the Jahn
Teller effect and of conformational analysis in simple alkanes, two examples where access to the complete CSD is necessary to accumulate sufficient structural data for analysis within a teaching experiment. In the current article, we describe further teaching modules that require use of the complete CSD System.

Published: May 06, 2011 891

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Table 1. Four Teaching Modules Based on Use of the Complete CSD Topic and Objectives of the Module

Interactive Activities

Unit 6: Molecular Dimensions (basic)

Search for SbCl6 ions in the CSD and retrieve all Sb
Cl bond lengths. What is the

Determine the preferred value of a Sb
Cl bond length in SbCl6 by generating a

typical Sb
Cl bond length in hexachloro
antimony? How precise is this mean

bond-length distribution from CSD structures. Evaluate the precision of the results

value? Investigate the outliers in the Sb
Cl bond length distribution. Evaluate the

using statistical criteria. Examine the outliers in the bond-length distribution and

structure that contains the longest observed Sb
Cl bond length.

attempt to distinguish those due to error from those of structural interest. Unit 7: Reaction Intermediates: Halonium Ions

Investigate the stereochemistry of halogen addition by searching for evidence in

To evaluate possible mechanisms for the electrophilic addition of Br2 to an alkene based on the stereochemistry of the products that are formed. To search the CSD

the CSD that the cyclic bromonium ion actually does exist. Find other examples of halonium ions. Explain the stability of the halonium ions found in the CSD.

for evidence of the existence of a cyclic bromonium ion intermediate. To account for the observed stability of the adamantylidene
adamantine
bromonium ion. Unit 8: Metal
Carbonyl Back Bonding

Define a search for molybdenum carbon monoxide complexes. Define the relevant

To search for molybdenum carbon monoxide complexes in the CSD using

bond lengths of interest (the Mo
C and CdO bonds) and apply suitable

ConQuest and monitor the Mo
C and CdO bond lengths. To read the search

constraints. Set the search running and analyze the results. Try to rationalize

results into Vista for further analysis. To rationalize the search results based on

your observations

electron counting and orbital considerations. Unit 9: Square-Planar to Tetrahedral Interconversions at 4-Coordinate Metals

Search for 4-coordinate transition metal complexes in the CSD and for each hit

Determine the preferred geometries adopted by 4-coordinate transition-metal

structure retrieve the values of the L-M-L angles (four “cis” and two “trans”). Work

complexes by analyzing the collected geometric data. Investigate some of the

out a single angular parameter to define the metal coordination geometry and plot

structures with nonidealized coordination geometries.

and analyze the data.

’ TEACHING MODULES THAT USE THE FULL CSD SYSTEM The “full system” CSD teaching modules currently available on the CCDC Web site3b are summarized in Table 1 in terms of their educational objectives and the interactive learning activities needed from the student. As with the modules based on the CSD teaching subset,2 the set of modules in Table 1 are a work in progress. They will be augmented with new material that will eventually be refined in a real teaching environment. Such work is already under way, as evidenced by the contributions made to a recent (Fall 2009) ACS Meeting Symposium on the educational uses of the CSD. The presentations at this symposium have been made available by the authors and can also be viewed on the CCDC Web site.3c In the examples below, we trace some important themes in modern organic and inorganic structural chemistry from an educational viewpoint. Some of the examples derive directly from published research applications of the CSD.

structures available in the CSD of the late 1980s. Ongoing spot checks show that these results have stood the test of time, and both of the tables5,6 contain much information that is important to today’s chemistry students. As an example of the determination of mean bond lengths in a teaching environment, we use the example of Sb
Cl bonds in SbCl6
ions. The relevant data are readily generated using ConQuest4 by encoding an Sb bonded to six Cl atoms in the graphical interface, and requiring that each Cl has a “total coordination number” of just one bonded atom (the Sb); this restriction eliminates the few examples of SbCl6
units that have extended connectivity through their Cl atoms. The following general search filters were also chosen from the ConQuest search menu: coordinates present in the CSD, crystallographic R (experimental precision) factor e0.075, no errors in the CSD entry, no crystallographic disorder, no catena bonding in the structure, no powder structures, and with the search restricted to metal
organic structures only. The six independent Sb
Cl distances in each discrete ion can be retrieved by ConQuest using the “add 3D” button. At the time of writing, this search yielded 321 discrete SbCl6
ions from 243 individual crystal structures, giving a total of 1926 Sb
Cl bonds for analysis. The bond-length distribution, shown in the histogram of Figure 1 and drawn using the Vista program,4 shows a sharp peak in the 2.25
2.45 Å region containing 97% of the observed data. However, in analyzing distributions of experimental results, it is important to examine any outlying observations. These tend to be of two types: (i) arising from errors or infelicities in the crystallographic experiment (e.g., poor resolution due to weakly diffracting crystals) and (ii) observations that are scientifically interesting and which may be chemically different from the majority of the distribution.

Example 1: Analysis of Mean Molecular Dimensions (Unit 6 of Table 1)

The determination of mean bond lengths was an early and important research application of the developing CSD. In the late 1980s, the CCDC and its collaborators generated two major printed compilations of mean bond lengths in organic structures,5 and in structures of the d- and f-block metals.6 These compilations replaced early listings published by the Chemical Society of London in 1958.7 By 2010, the two newer compilations had together received more than 7,500 citations in the scientific literature, being used principally to validate novel crystal structure results or to build 3D model molecules. The organic and metal
organic bond lengths were generated by careful chemical and statistical analysis of data from some 28,000 892

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Figure 1. Histogram of Sb
Cl bond lengths from the CSD; note the outliers around 1.8 Å, and at g2.6 Å which are explained in the text.

Figure 3. Distribution of iron
nitrogen bond distances in 6-coordinate (octahedral) Fe(LN) complexes.

The second set of outliers with Sb
Cl bonds g2.6 Å comprises five structures, all of which contain strong N
H 3 3 3 Cl
Sb hydrogen bonds. Examination of the published reports shows that these five structures are the only CSD entries that contain the rarer SbIIICl63
trianion8 rather than the more usual SbVCl6
monoanion that dominates the observed distribution. It is therefore valid to eliminate all 54 of these outliers to give Figure 2, the distribution of SbVCl6
bond lengths originally intended by the CSD analysis. Even here, one entry has rather shorter bond lengths and may be eliminated on statistical grounds to give a mean Sb
Cl bond length of 2.362 Å with a standard deviation of the mean of 0.001 Å, and a sample standard deviation of 0.010 Å for 1871 remaining observations. Example 2: High-Spin versus Low-Spin Complexes (New Unit under Development)

Octahderal iron(III), a d5 system, can adopt both high-spin and low-spin forms and crystal-field stabilization-energy diagrams can be used to account for these states.9 Importantly, their effects on ligand binding can be readily exemplified using crystal structure data. Students can be asked to use ConQuest to search the CSD for compounds that have at least one sp3hybridized nitrogen atom bound to a 6-coordinate iron. A subsequent plot of the Fe
N distances for all the located structures is bimodal (Figure 3). A majority of Fe
N distances are between 2.12 and 2.34 Å and these are the high-spin complexes. The low-spin complexes have Fe
N distances between 1.9 and 2.10 Å and are slightly less common. In comparison, for octahedral nickel(II), a d8 system, only highspin complexes are known and a mean Ni
N distance of 2.116 Å is found (see Figure 4). Although 6-coordinate (octahedral) nickel(II) complexes adopt the high-spin state exclusively, further investigations of five-coordinate (trigonal-bipyramidal and square-pyramidal) and four-coordinate (square-planar) geometries can be used to show that low-spin nickel complexes also exist. Such searches are easily defined within ConQuest by requiring that the metal be bound to

Figure 2. Histogram of Sb
Cl bond lengths from the CSD after removal of outliers identified in Figure 1.

By probing the results of Figure 1, students discover that both effects are in operation here. Two small sets of distant outliers can be seen: 24 Sb
Cl bonds in the 1.8
1.9 Å region, and a further 30 bonds having Sb
Cl g 2.6 Å. Examination of the published reports for the three crystal structures that generated the 24 short bonds indicates that the ion involved in each case was more likely to have been SbF6
for which a mean Sb
F bond length of 1.846(1) Å can readily be derived from the CSD, almost identical to the position of the shorter outliers of Figure 1. It appears that the atoms bonded to Sb in these three crystal structures have either been reported erroneously as Cl or may even have been included in the structural model as Cl. The CCDC is currently contacting the authors of these reports so that we may correct the CSD entries. 893

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Figure 6. Adamantylidene
adamantane
bromonium tribromide [CSD reference code DAKVUG]. Severe steric crowding at the face of the bond that is opposite to the Brþ atom prevents access of a nucleophile and thus stabilizes the bromonium ion. The adamantyl H atoms that block the nucleophiles approach are shown in spacefill display style.

Figure 4. Distribution of nickel
nitrogen bond distances in 6-coordinate (octahedral) Ni(LN) complexes. Figure 7. Catena H bonding in acetic acid [CSD reference code ACETAC0713].

existence of reaction intermediates, and this is provided by the CSD in the form of three halonium ion structures that are all adamantylidene
adamantane derivatives; two bromonium ions (DAKVUG and WEVPIW) and one iodinium ion (WEVPOC) are retrieved in a ConQuest search for C
C
halogenþ threemembered rings. The structure of DAKVUG12 is illustrated in Figure 6. The question then arises as to why these halonium ions are stable enough to be characterized by X-ray crystallography, and the answer lies in the severe steric overcrowding on the face of the bond that is opposite to the Brþ, as shown in Figure 6, with three pairs of adamantyl H atoms having nonbonded contacts in the range 2.00
2.15 Å. Thus, neither side of the C
C bond is now open to attack by Br
, and the bromonium ion is sufficiently stabilized for the X-ray experiment.

Figure 5. Mechanism for electrophilic addition of Br2 to an alkene.

a specific number of atoms. A similar search with nickel constrained to be square-planar (low-spin) yields a mean Ni
N(sp3) distance of 1.945 Å. These square-planar nickel(II) complexes can be located in the CSD by constraining the nickel ion to be 4-coordinate and selecting only those structures that have a L
Ni
N angle in the range 85
95°, where L is any possible ligand atom type. Further ideas for an open-ended discovery assignment involving the high-spin and low-spin forms of nickel(II) and their geometries are outlined by Zimmer et al.10

Example 4: Hydrogen Bonding (New Unit under Development)

The hydrogen bond is the crucial noncovalent interaction involved in molecular recognition in supramolecular chemistry, in the structural stabilization of biological macromolecules and their interactions with active ligands, and in determining the extended molecular packing arrangements in a crystal lattice. Crystal structure data are therefore central to our understanding of hydrogen bonds and other nonbonded interactions. No other technique provides such precise metrical and spatial descriptions of intermolecular interactions and, since its inception, the CSD has been a vital information source, contributing information to many hundreds of research articles and several monographs. It is therefore vital that students in chemistry and the biological sciences gain a good basic understanding of the structural implications and geometrical descriptions of H bonds, Dδ

Hδþ 3 3 3 Aδ
, in which an electronegative atom (D) donates an electropositive H atom to form an interaction with an electronegative acceptor (A). At an introductory level, CSD structures can be used in Mercury4 to illustrate the formation of catena H bonds in acetic

Example 3: Halonium Ion Reaction Intermediates (Unit 7 of Table 1)

The stereospecific electrophilic addition of halogens to simple nonconjugated alkene nucleophiles to form a trans-alkane product is a fundamental component of undergraduate organic chemistry courses. The mechanism proceeds in two stages,11 as shown in Figure 5 for cyclopentene: (i) cleavage of the weak Br
Br bond and addition of Br across the CdC bond to form a bromonium ion (the C2Brþ ring) together with a residual Br
ion, followed by (ii) attack by Br
on the unprotected face of the bromonium ion to yield only the trans-dibromocyclopentane product. This mechanism is consistent with the observed stereochemistry of the products of halogen addition. Formation of the cisproduct is precluded due to the shielding afforded by the bromonium Brþ on one side of the double bond. For students, it is useful to be able to show experimental evidence for the 894

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Figure 11. Geometrical parameters used to describe N
H 3 3 3 O H bonds in amides. Figure 8. H-bonded carboxylic acid dimers in propionic acid [CSD reference code PRONAC14].

Figure 12. ConQuest query to locate N
H 3 3 3 O hydrogen bonds in amides.

N
H and a fully delocalized carboxylate in, for example, which then generates the complex 3D pattern of H bonds shown in Figure 10. Again, one of the N
H donors is bifurcated, and both carboxylate-O atoms accept two H bonds. Thus, Figure 10 begins to illustrate the complexity of H-bonding possibilities in proteins. The CSD is frequently used to study the general geometrical characteristics of specific H bonds, and for this, the complete CSD is required to obtain results that are of statistical value. In this module, we concentrate on N
H 3 3 3 O hydrogen bonds found in amides and related compounds and which are typical of many H bonds found in biological systems. The geometrical parameters used to describe each bond are shown in Figure 11, whereas a typical ConQuest search query is shown in Figure 12. The geometrical parameters retrieved by ConQuest have been analyzed using Vista, and the results are presented graphically in Figures 13
15. The histogram of the H-bond length d(H 3 3 3 O) in Figure 13 shows a normal distribution with a clearly defined peak well below the sum of van der Waals radii for H and O (2.75 Å). The mean d(H 3 3 3 O) is 2.11 Å, 0.64 Å shorter than the sum of van der Waals radii and 1.14 Å longer than the sum of covalent radii for H and O. The scatterplot of d(H 3 3 3 O) versus the N
H 3 3 3 O angle (theta) shown in Figure 14 is of significant interest. First, it shows the strong preference for linearity (θ = 180°) of the H-bonded N
H 3 3 3 O system, and second it shows that the shorter (stronger) H bonds are the most linear. Indeed, there is a clear tendency for the longer bonds to occur at θ values that deviate most from linearity. A recent study17 using high-level ab initio calculations of H-bond interaction energies has shown that the H-bond strength decreases dramatically as θ decreases from 180°, and this is clearly reflected in Figure 14. Directionality at the acceptor O atom is also an important feature of this system, and the polar histogram of Figure 15 shows that the approach of donor H to the acceptor is closely aligned to the O lone pair direction, a factor recognized in early statistical analyses of H bonding to O acceptors.18 Finally, we have calculated the angle χ, the angle between the donor N
H vector and the plane of the amide group containing the acceptor O atom, and the histogram of χ (Figure 16) shows that N
H has a strong preference to approach the acceptor in the amide plane. L-alanine,

Figure 9. H-bonded layers in 2-methoxybenzamide [CSD reference code RECQIA15] .

Figure 10. Complex H-bond system in L-alanine [CSD reference code LALNIN16].

acid (Figure 7) that may be contrasted with the H-bonded dimer formed by propionic acid (Figure 8) and many other simple acids. However, the presence of even one additional donor H in, for example, simple amides can lead to much more complex H-bonding patterns such as the 2D H-bonded molecular layers in 2-methoxybenzamide (Figure 9). Thus, Figure 9 illustrates several common features of complex H-bonded systems: (i) an intramolecular H bond involving an amido-N-H donor and methoxy-O acceptor, (ii) involvement (bifurcation) of that amido N
H in two H bonds, one intramolecular and the other intermolecular, and (iii) acceptance of an H bond by both lone pairs of the benzamide CdO group. [The reader might like to compare and contrast Figure 9 with the H-bonding pattern in benzamide, which was illustrated in part 3 of this series4]. The availability of additional donors and acceptors increases the H-bonded structural complexity to the level observed in simple amino acids. Amino acids exist as zwitterions, giving three donor 895

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Figure 15. Polar histogram of j, the angle H 3 3 3 OdC, showing the H-bond directionality at the O acceptor. (j is fully spelled here since Vista has no provision for representing Greek characters). Figure 13. Histogram of the H 3 3 3 O H-bond length in amides.

Figure 14. Scatterplot of the H 3 3 3 O distance versus the N
H 3 3 3 O angle (θ is fully spelled here since Vista has no provision for representing Greek characters).

The simple CSD study of H bonding in amides gives students a good grounding in the basics of H-bond geometry, and many other systems can be examined using experimental data in a similar manner. Such studies are particularly valuable in providing background understanding of the topic for those students who wish to become involved in the understanding and interpretation of biological structures. Indeed, combining CSD studies of this type with studies of protein crystal structures contained in the Protein Data Bank19 provides an excellent basis for instruction in structural biology.

Figure 16. Histogram of the angle χ between the N
H vector and the amide plane containing the acceptor O atom (χ is fully spelled here since Vista has no provision for representing Greek characters).

’ CONCLUSIONS This article has described four teaching modules that require use of the complete CSD, now containing more than half a million small-molecule crystal structures, together with the extensive software tools contained in the distributed CSD System. As with the earlier examples presented in this series of articles2,4 and elsewhere,20 we have tried to choose topics that are fundamental to the chemistry curriculum. When combined with other published educational applications of the CSD10,21
23 and with the work presented at the Fall 2009 ACS Symposium3c on this topic, the fundamental importance of crystal structure information in the chemistry classroom is now clearly recognized,24 896

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particularly as a basis for discovery-based learning. Our current aim is to extend the range of teaching modules that are available3b and to continue to find new ways to develop the CSD and its associated software tools as a major resource in chemical education.

(23) Reglinski, J.; Graham, D.; Kennedy, A. R.; Gibson, L. T. J. Chem. Educ. 2004, 81, 76–82. (24) Coleman, W. F. J. Chem. Educ. 2010, 87, 882–883.

’ AUTHOR INFORMATION Corresponding Author

*E-mail: [email protected].

’ ACKNOWLEDGMENT The teaching examples described above are based on work supported by the United States National Science Foundation under Grant No. 0725294. ’ REFERENCES (1) Battle, G. M.; Allen, F. H.; Ferrence, G. M. J. Chem. Educ. 2010, 87, 809–812. (2) Battle, G. M.; Allen, F. H.; Ferrence, G. M. J. Chem. Educ. 2010, 87, 813–818. (3) (a) Allen, F. H. Acta Crystallogr. 2002, B58, 380–388. (b) Cambridge Structural Database (CSD) for Teaching. http:// www.ccdc.cam.ac.uk/free_services/teaching (accessed Apr 2011). (c) CCDC ACS Symposium Web site. http://www.ccdc.cam.ac.uk/ free_services/teaching/ACS symposium (accessed Apr 2011). (4) Battle, G. M.; Allen, F. H.; Ferrence G. M. J. Chem. Educ. 2010 88, (DOI: 10.1021/ed1011019). (5) Allen, F. H.; Kennard, O.; Watson, D. G.; Brammer, L.; Orpen, A. G.; Taylor, R. J. Chem. Soc., Perkin Trans. 2 1987, S1–S19. (6) Orpen, A. G.; Brammer, L.; Allen, F. H.; Kennard, O.; Watson, D. G.; Taylor, R. J. Chem. Soc., Dalton Trans. 1989, S1–S83. (7) Sutton, L. E., Ed. Tables of Interatomic Distances and Configuration. In Molecules and Ions: The Chemical Society: London, U.K., 1958. (8) Pedrosa, T. J.; Orpen, A. G. Cryst. Growth Des. 2005, 5, 681–693. (9) Atkins, P; Jones, L. Chemical Principles: The Quest for Insight, 5th ed.; The d-Block: Metals in Transition; W. H. Freeman: New York, 2010; Chapter 16. (10) Davis, T. V.; Zaveer, M. S.; Zimmer, M. J. Chem. Educ. 2002, 79, 1278–1280. (11) Clayden, J.; Greeves, N.; Warren, S.; Wothers, P. Organic Chemistry; Oxford University Press: Oxford, U.K., 2000. (12) Slebocka-Tilk, H.; Ball, R. G.; Brown, R. S. J. Am. Chem. Soc. 1985, 107, 4504–4508. (13) Jones, R. E.; Templeton, D. H. Acta Crystallogr. 1958, 11, 484–487. (14) Strieter, F. J.; Templeton, D. H.; Scheuerman, R. F.; Sass, R. L. Acta Crystallogr. 1962, 15, 1233–1239. (15) Moribe, K.; Tsuchiya, M.; Tozuka, Y.; Yamaguchi, K.; Oguchi, T.; Yamamoto, K. J. Inclusion Phenom. Macrocyclic Chem. 2006, 54, 9–16. (16) Simpson, H. J.; Marsh, R. E. Acta Crystallogr. 1966, 20, 550–555. (17) Wood, P. A.; Allen, F. H.; Pidcock, E. CrystEngComm 2009, 11, 1563–1571. (18) Murray-Rust, P.; Glusker, J. P. J. Am. Chem. Soc. 1984, 106, 1018–1025. (19) Dutta, S.; Zardecki, C.; Goodsell, D. S.; Berman, H. M. J. Appl. Crystallogr. 2010, 43, 1224–1229. (20) Battle, G. M.; Ferrence, G. M.; Allen, F. H. J. Appl. Crystallogr. 2010, 43, 1208–1223. (21) Wackerly, J. W.; Janowicz, P. A.; Ritchey, J. A.; Caruso, M. M.; Elliot, E. L.; Moore, J. S. J. Chem. Educ. 2009, 86, 460–464. (22) Yuriev, E.; Chalmers, D.; Capuano, B. J. Chem. Educ. 2009, 86, 477–478. 897

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