On the Web edited by
William F. Coleman Wellesley College Wellesley, MA 02481
Comparing Solid, Gas Phase, and Solution Structures Using the Cambridge Structural Database William F. Coleman Department of Chemistry, Wellesley College, Wellesley, Massachusetts 02481
[email protected] w This paper contains enhanced objects available on the Internet at http://pubs.acs.org/jchemeduc. n
JCE Featured Molecules for August 2010 The process of producing this column begins when Mary Saecker, the JCE Production Manager, sends me one or more papers from an issue that she feels contain molecules that might be interesting to include in the column and in the molecule collection (1). The number of papers can range from one or two to many. I then choose the paper(s) to focus on, and proceed from there. When I received the copy for this month's issue, I immediately chose the two papers by Gary Battle, Frank Allen, and Gregory Ferrence describing the teaching subset of the Cambridge Structural Database (CSD) and associated teaching modules (2, 3). I made this choice because this database is an important molecule collection that can serve as the source of many instructive assignments, and because I have been using the full CSD in my inorganic chemistry course for a number of years, and used the CSD Teaching Subset for the last two iterations of the class. A vast majority of structures in the JCE Featured Molecules Collection (1) have been generated computationally using Hartree-Fock or higher level calculations. These structures represent the best models of isolated gas phase species in the absence of structures from more conventional experiments. Access to the CSD Teaching Subset allows students to compare structures of species in the solid state to those calculated in the gas phase or in solution (4). I received the materials for this month two days prior to our Commencement, and managed to corral two graduating seniors who had taken the inorganic class to look at the material with me. As they looked through the examples, they were intrigued to notice that the five-membered ring in caffeine, in file CAFINE, was not planar, and wondered whether the same was true in the gas phase or in solution. Density functional calculations using the B3LYP functional and 6311þþG(d,p) basis sets confirm that both rings are planar (and they are coplanar) in the gas phase, and in water using an integral equation formalism-polarizable continuum model (IEF-PCM) in Gaussian 09. Additionally, the gas phase and solution structures are identical within computational error. Students with access to the complete CSD will find 61 structures containing caffeine, including a number with nonplanar rings and a number in which caffeine is acting as a ligand. My students were also interested to see cyclopentane assuming different conformations in the files LISLOO and IHIPOE. Figure 1 shows the bond lengths and angles in those forms. Optimization of the two forms at the DFT-B3LYP6311þþG(d,p) level results in a single structure, with bond lengths and angles in Figure 2. The file IHIPOE also shows a very
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Figure 1. Bond lengths and angles and ball-and-stick representations of cyclopentane from crystal structures IHIPOE and LISLOO, respectively (4).
Figure 2. Bond lengths and angles and ball-and-stick representations of cyclopentane resulting from optimization of the structures in Figure 1 at the DFT/B3LYP-6311þþG(d,p) level.
distorted hexafluorophosphate anion, which, as expected, computes to a perfect octahedron in the absence of crystal packing forces. Table 1 lists the 3D, rotatable images in MOL format of the molecules available in the HTML version of this paper. As is often the case, a number of the two-dimensional diagrams in the database would lead a student to an incorrect prediction of the three-dimensional structure. Several cases are found in the files YALROS, TANWAG, and ROLSEQ, where various species appear in forms that violate the predictions of the VSEPR model.
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Vol. 87 No. 8 August 2010 pubs.acs.org/jchemeduc r 2010 American Chemical Society and Division of Chemical Education, Inc. 10.1021/ed1006162 Published on Web 06/25/2010
On the Web Table 1. JCE Featured Molecules for August 2010 Featured Molecule
Description
caffeine (gas phase)
density functional calculations using the B3LYP functional and 6311þþG(d,p) basis sets
caffeine (water)
density functional calculations using integral equation formalism-polarizable continuum model (IEF-PCM) in Gaussian 09a
cyclopentane (IHIPOE)
cyclopentane from the crystal structure IHIPOE
cyclopentane (LISLOO)
cyclopentane from the crystal structure LISLOO
cyclopentane (optimized)
optimization of the forms of cyclopentane at the DFT-B3LYP-6311þþG(d,p) level
The three-dimensional structures in these species show that the predictions of VSEPR theory are found in the crystal structures. The CSD Teaching Subset is an excellent addition to the growing pantheon of readily accessible, interactive, three-dimensional structures available for use in teaching chemistry. The authors have suggested a valuable set of exercises, and comparison of the crystal structures with those in the gas phase and solution enable students to explore the effects of packing forces, and to test a number of their models of molecular structure. Literature Cited 1. JCE Featured Molecules from June 2002 through December 2009 are available at the JCE Digital Library, http://www.jce.divched.org/ JCEWWW/Features/MonthlyMolecules/ (accessed Jun 2010). JCE
r 2010 American Chemical Society and Division of Chemical Education, Inc.
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Featured Molecules from January 2010 to the present are available in the HTML version of each column. 2. Battle, G. M.; Allen, F. H.; Ferrence, G. M. Teaching ThreeDimensional Structural Chemistry Using Crystal Structure Databases: Part 1, an Interactive Web-Accessible Teaching Subset of the Cambridge Structural Database. J. Chem. Educ., 2010, 87, DOI: 10.1021/ed100256k. 3. Battle, G. M.; Allen, F. H.; Ferrence, G. M. Teaching ThreeDimensional Structural Chemistry Using Crystal Structure Databases: Part 2, Teaching Units That Utilize an Interactive WebAccessible Subset of the Cambridge Structural Database. J. Chem. Educ., 2010, 87, DOI: 10.1021/ed100257t. 4. The Cambridge Structural Database Teaching Subset Home Page is available at http://webcsd.ccdc.cam.ac.uk/teaching_database_demo. php (accessed Jun 2010).
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