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A section of ChemPrime, the Chemical Educations Digital Library's free General Chemistry textbook.
Molecular Models of Annatto Seed Components   
(Interactive Simulation (1))
In January 2008 the focus of this column was on the plant pigments lycopene and beta-carotene (1). Our attention this month returns to two papers discussing the pigments in annatto seeds (Figure 1), including direct precursors to lycopene. The paper by Teixeira, Dur�n, and Guterres describes the extraction and encapsulation of annatto seed components (2). The McCullagh and Ramos paper describes the separation of the pigment bixin from these seeds by TLC and column chromatography (3). These molecules could form the basis of interesting exercises across the chemistry curriculum. In courses designed for non-majors, students could choose a molecule from the table and search the literature for both scientific and non-scientific sources. Are the claims made in the latter sources regarding the health benefits of these molecules consistent with the scientific data? That discussion could be expanded to the more general question of how one tests the validity of statements made in what are essentially advertisements. Are any of these precursor molecules to lycopene considered to have anticancer properties (4)? In introductory or general chemistry courses, students could explore the various bond lengths and bond angles in the molecules to see whether they are consistent with their expectations based on simple bonding models. In introductory, organic, or biochemistry classes, the thermodynamics of hydrogenation and dehydrogenation could be examined. This might make an interesting alternative to the oft-discussed Haber Process. What conditions would one propose for a dehydrogenation process? Why are dehydrogenation reactions important? What enzymes catalyze the various dehydrogenation steps from phytoene to lycopene? These molecules could also be used in a variety of computational exercises in introductory and physical chemistry courses. Hartree�Fock calculations on a molecule such as phytoene may prove time-consuming depending on the nature of the computing system available. A good place to begin would be to perform semi-empirical calculations on the various molecules. Do the optimized structures match experimental results or the results of larger calculations? Does the HOMO�LUMO gap correlate with the observed electronic absorption spectra? Which is more important in determining the difference in absorption between phytoene and phytofluene, the total number of double bonds or the number of bonds in the region of conjugation? Of course the aspect of these molecules that is most likely to capture student attention is their color, and they provide nice examples of the origin of color, the relationship between color observed and color absorbed, and, in upper level courses, the more detailed relationships of the energies of the ground and excited states.
Molecular Models of Lycopene and Other Carotenoids   
(Interactive Simulation (1))
Over the past decade or so the phrase emerging research suggests has entered the argot of advertising, and that phrase has been applied to this month's Featured Molecule, lycopene, particularly with regard to potential health benefits of tomatoes. The paper by Jie Zhu, Mingjie Zhang, and Qingwei Liu (1) describes an extraction and purification of lycopene from tomato paste using an emulsion rather than the traditional solvent-based extraction. Lycopene is a member of the family of molecules called carotenoids, the most familiar of which is beta-carotene. This family of natural products includes more than 500 members that have been isolated and whose structures have been determined. Professor Hanspeter Pfander's research group at the University of Bern maintains a Web site with a significant amount of information on carotenoid structure, synthesis, and activity (2). Structurally one can think of carotenoids as consisting of three segments, a relatively rigid conjugated central portion with end groups. The end groups are, in general, flexible with respect to rotation about the bond connecting them to the central portion. For example, in beta-carotene, the dependence of total energy on the dihedral angle shown in Figure 1, displays a very broad range of essentially isoenergetic conformations (Figure 2). The energies shown in Figure 2 were calculated at the PM3 level using Hyperchem 7.5 (3). Calculations at the HF/631-G(d,p) level, with many fewer data points, show a similar trend. Many of the health benefits derived from various carotenoids are attributed to their antioxidant activities. Carotenoids react with singlet-oxygen in a physical, diffusion-controlled, quenching process that results in ground state triplet-oxygen and, following a non-radiative relaxation, ground state carotenoid. Of the various carotenoids that have been studied, lycopene and beta-carotene show the greatest quenching rate constants (4). The carotenoids provide us with countless explorations by students and teachers looking for connections between fundamental chemical concepts and real-world applications. Structure, reactivity, chemical synthesis, biosynthesis, and stereochemistry are just a few of the concepts involved in understanding the manifest important roles that these molecules play.
Molecular Models of Resveratrol   
(Interactive Simulation (1))
The featured molecules this month are from the paper "Resveratrol Photoisomerization: An Integrative Guided-Inquiry Experiment" by Bernard, Gernigon, and Britz-McKibbin exploring trans to cis photoisomerization in resveratrol. Examination of Figure 1 in that paper, where the hydrogen atoms have been omitted, might lead one to conclude that the structures are relatively straightforward. These isomers provide students an excellent opportunity to test their ability to take a two-dimensional representation and envision the three-dimensional structure of the molecule and to consider the competing factors that might lead to the three-dimensional structures being non-planar. The two-dimensional models focus attention on the possibility of extended pi-electron delocalization. Addition of the hydrogen atoms clearly suggests that delocalization will compete with non-bonded H-H repulsions in the cis isomer. Further examination of the trans isomer shows that such non-bonded interactions are, in what one might call a first-order approximation, like those in biphenyl interactions that lead biphenyl to be non-planar in both the gas phase and in a variety of solvents. The backbone of the trans isomer of resveratrol, trans-stilbene, has been the subject of a number of theoretical and experimental investigations (1, 2). In general, Hartree-Fock calculations predict a non-planar geometry for this molecule while Density Functional Calculations, using the same basis sets, predict an essentially planar structure. Spectroscopic evidence supports a temperature-dependent structure for trans-stilbene with the molecule being planar at low temperature and non-planar at high temperatures. Our calculations on trans-resveratrol produce similar results. Hartree-Fock calculations using the 6-31G** (6- 31G(d,p)) basis set predict a dihedral angle of approximately 24 degrees between each ring and the central carbon-carbon double bond. This result is consistent with the reported value of 23 degrees using the 6-31G* basis set. We also find that DFT calculations using the B3LYP functional and the 6- 31G** basis set, lead to a planar configuration. We include several versions of trans-stilbene and trans-resveratrol in the molecule collection so that students can explore these structural questions in more detail. For each molecule, structures obtained from PM3, HF(6-31G**), and DFT(B3LYP/6-31G**) calculations are included, as well as planar and non-planar structures of biphenyl. Measurement of the various bond and torsion angles using Jmol will help students develop a sense of the distance dependence of the non-bonded interactions and their importance in determining the actual structure. They might also wish to consider what additional degree(s) of freedom resveratrol and stilbene have that biphenyl does not, allowing the trans-form of the former molecules to remain planar under certain conditions, while minimizing the effect of the non-bonded repulsions.
Molecular Models of Leaf Extracts   
(Interactive Simulation (1))
Our Featured Molecules this month come from the paper by Pelter et. al. on the analysis of leaf extracts by thin-layer chromatography (1). As the authors discuss, their experiment may be used in courses at various levels of the curriculum. The molecules discussed in the paper are also of wide interest both for their structural properties and their wide-ranging appearance in both natural and synthetic substances. Included in the molecule collection are all of the isomers for the molecules pictured in the text with the exception of menthyl acetate, for which only one structure is given (see below). All of these molecules have been optimized at the HF/631-G(d) level. The menthol family enantiomeric pairs of menthol, isomenthol, neomenthol and neoisomenthol provide a rich yet coherent group of molecules on which to base discussion of chirality, enantiomers and diastereomers. Treadwell and Black have described some of the differences in physical properties of four members of this family, and several other experiments using one or more menthols have been published in this Journal (2, 3). I have created a Web page in which the eight molecules are embedded in no particular order, and with no rational file names. This is being used in at least one of our organic sections to give students experience at identifying enantiomers, and diastereomers, and in applying R/S notation (4). As access to computational software becomes more common, and as efforts are being made to incorporate more relevant modeling experiments into all levels of the curriculum, the menthols again present some interesting possibilities. While students at the organic level know about enantiomers differing in their optical rotation, and about chiral molecules interacting with chiral and achiral environments, it is instructive for them to think of other ways in which enantiomers and diastereomers are the same or different. Three useful ways of checking to see whether two structures are truly enantiomers is to compute their total energies, vibrational spectra, and dipole moments. These calculations are available in most common computational packages. Figure 1 shows the results of energy calculations on optimized structures of the eight isomers. The enantiomeric pairs have, as expected, exactly the same total energy, while the various diastereomers differ in energy. The computation of the vibrational spectra is a very sensitive probe to determine whether two structures are optimized and enantiomeric or not. Structures that are almost enantiomeric, but not quite optimized, may exhibit similar energies, but the low frequency vibrations will be sensitive to any deviation from optimization. If two supposedly enantiomeric structures do not have the same computed vibrations, or if either shows a negative frequency, the structures need to be optimized more carefully. As with the vibrational frequencies, enantiomers should show identical dipole moments. Only one structure of the eight isomers in the menthyl acetate family is included in the collection, giving students the chance to build the other seven and verify their computed properties. Because of the central role that chirality plays in chemistry, and particularly in biochemistry, it seems appropriate to introduce some of these visualization and modeling exercises early in the curriculum, and in courses designed for students majoring in other areas. Students in various courses could pursue other aspects of these same molecules including odor and cooling properties, and green chemistry approaches to synthesizing menthols.
The World's Clothing Supply   
(Article (36))
Volume 05, issue 15 of a series of leaflets covering subjects of interest to students of elementary chemistry distributed in 1929 - 1932.
The World's Clothing Supply   
(Article (36))
Volume 04, issue 14 of a series of leaflets covering subjects of interest to students of elementary chemistry distributed in 1929 - 1932.
The World's Clothing Supply   
(Article (35))
Volume 03, issue 15 of a series of leaflets covering subjects of interest to students of elementary chemistry distributed in 1929 - 1932.
The World's Food Supply   
(Article (34))
Volume 03, issue 09 of a series of leaflets covering subjects of interest to students of elementary chemistry distributed in 1929 - 1932.
The Zinc Family   
(Article (34))
Volume 03, issue 22 of a series of leaflets covering subjects of interest to students of elementary chemistry distributed in 1929 - 1932.
Planet Earth   
(Activity, Instructional Material (9), Test, Assessment Material (6), Instructional Material (3))
ACS Science for Kids activities and tests exploring applications of chemistry on Earth.
Plants-ACS Science for Kids   
(Activity, Instructional Material (8))
ACS Science for Kids activities exploring the properties and chemistry of plants.
(Activity, Instructional Material (7))
ACS Science for Kids activities explore the aspects of recording scientific data and presenting that data in useful graphs.
Characteristics of Materials   
(Activity, Instructional Material (7), Test, Assessment Material (15))
What makes diapers absorbent? Is peanut butter stickier than syrup or jelly? Strong, stretchy, sticky, or sweet—everything around us has special properties which make them unique. See if you can identify and compare the characteristics of materials.
(Activity, Instructional Material (11))
ACS Science for Kids activities that explore the chemical properties of foods.