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JCE Featured Molecules
William F. Coleman Wellesley College Wellesley, MA 02481
Fountain Pen Ink October Featured Molecules This month’s Featured Molecules are drawn from the paper on page 1476 by J. Martín-Gil, M. C. Ramos-Sánchez, F. J. Martín-Gil, and M. José-Yacamán on the composition and stability of inks. The range of species mentioned in the paper is well illustrated with interactive three-dimensional structures. For the hydroxyl and hydroperoxyl radicals and the superoxide ion we have calculated highly accurate structures at the MP2/6-311++G(3df,3pd) level, and for gallic acid at the DFT/6-31G(d) level. The gallotannic acid was modeled by molecular mechanics methods using the Amber-99, UFF, and MM+ force fields. The resultant structure is dependent on the choice of initial geometry and on the force field used. Several different representations of gallotannic acid are included in the molecule collection. One representation begins by applying simple VSEPR arguments to the structure shown in the paper, and it lends 3-dimensionality to the “arms” of the molecule and the stereochemistry around the central 6-membered ring. Several additional structures modeled with molecular mechanics from different starting geometries appear to be quite different from one another. The interesting stacking of aromatic rings on adjacent “arms” appears in all calculations, and the degree of stacking influences the MM energy—the more stacking, the lower the energy, but the range of differences in energies of a number of similar conformations is less than 15 kcal/mol. This molecule is a useful way to introduce students to the ambiguities and capabilities inherent in molecular modeling. Given the ambiguities around the gallotannic acid structure, should we avoid showing such structures to students? A common argument is that many students may incorrectly take a computer-calculated structure as “truth”. However, by constantly exposing students to a range of 3-dimensional structures, we help them develop a tool kit to interpret the
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Journal of Chemical Education
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gallic acid
structure. It is useful to help students learn that the chymist should indeed be skeptical. For beginning students, or those in non-majors courses, the radicals involved in ink stabilization and deterioration are also relevant to atmospheric chemistry and deleterious biological processes such as aging. For many introductory chemistry students, the first and only time they encounter a species such as the superoxide ion is when they are asked to use simple MO theory to predict bond lengths and bond orders in a series of ions of dioxygen. The molecule collection for this month includes structures for all such ions ranging from O22+ to O22- and the bond lengths are easily measured in the Jmol form. Changing the names of the molecule files to something anonymous would then allow the usual question to be phrased differently as “Here are interactive structures of five dioxygen species ranging from O22+ to O22᎑. Measure the bond length in each, decide which species it is, and use MO theory to support your assignment.” Fully manipulable (Chime and Jmol) versions of gallic acid, gallotannic acid, ions ranging from O22+ to O22᎑, as well the other molecules in the collection are available at the JCE Digital Library Web site: http://www.JCE.DivCHED.org/JCEWWW/Features/ MonthlyMolecules/2006/Oct
Vol. 83 No. 10 October 2006
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www.JCE.DivCHED.org
