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11 Journal Articles
18 Other Resources
Journal Articles: First 3 results.
Molecular Models of Natural Products  William F. Coleman
This months Featured Molecules focus on natural products and include blattellquinone, a sex pheromone secreted by female German cockroaches to attract males, and (R)-limonene, a secondary metabolite found in citrus fruit peels.
Coleman, William F. J. Chem. Educ. 2008, 85, 1584.
Molecular Modeling |
Molecular Properties / Structure |
Natural Products
Identification of Secondary Metabolites in Citrus Fruit Using Gas Chromatography and Mass Spectroscopy  Jean-Michel Lavoie, Esteban Chornet, and André Pelletier
Using a simple extraction and a gas chromatograph coupled with a mass spectrometer, this protocol allows students in analytical or organic chemistry to quantify and qualify monoterpenes from the peels of limes, grapefruits, and oranges.
Lavoie, Jean-Michel; Chornet, Esteban; Pelletier, André. J. Chem. Educ. 2008, 85, 1555.
Alkenes |
Food Science |
Gas Chromatography |
Mass Spectrometry |
Natural Products |
Plant Chemistry |
Qualitative Analysis |
Quantitative Analysis
Identifying Softwoods and Hardwoods by Infrared Spectroscopy  Brady Barker and Noel L. Owen
Infrared spectra of 45 softwoods and hardwoods have been recorded. The wavenumber values of the carbonyl stretching vibration and one of the ring-breathing modes of lignin are used to distinguish softwoods from hardwoods. The differences between the absorption bands for the softwoods and hardwoods in each instance are shown to be statistically significant.
Barker, Brady; Owen, Noel L. J. Chem. Educ. 1999, 76, 1706.
Carbohydrates |
Instrumental Methods |
IR Spectroscopy |
Plant Chemistry |
Molecular Properties / Structure
View all 11 articles
Other Resources: First 3 results
Molecular Models of Natural Products  William F. Coleman
This month's issue of the Journal includes several papers discussing interesting molecules that fall into the broad category of natural products, and four of these papers serve as the source for our featured molecules this time around. Addison Ault weaves an interesting tale of the search for the true structure of eserethole and of the competition between two research groups that of Percy Julian, consisting of two people, and that of the British chemist Robert Robinson, a large group at Oxford (1). David Vosburg describes a case study approach to teaching organic synthesis and includes a number of molecules that have been the basis of student research papers (2). Jean-Michel Lavoie, Esteban Chornet, and André Pelletier have developed an experiment utilizing GCMS to separate terpenes from citrus (3), and Patty Feist, in a paper that may send readers running for their Kafka, has students synthesize a cockroach pheromone that may have wide applicability in cockroach control without the problems created by many insecticides (4).The molecules that have been added to our collection contain a wide variety of functional groups, and would serve as a good source for an exercise in having students recognize these functional groups in a number of different settings. Questions such as How many cyclic ether groups are present?, How many bridgehead carbons?, or How many chiral centers would be useful exercises in organic and introductory non-majors courses. Students could find other pheromone structures and see how they compare with that of blattellaquinone, or explore the various ways in which the steroid backbone shows up in the collection.This collection of molecules also provides a good starting point for students to use the capabilities of Jmol to further explore structural features. The focus here is on measuring bond distance and angles. Double clicking on any atom will change the cursor to a cross-hair (this may take a little practice). One end of a dashed line is now locked to that atom. Dragging the free end of the line to other atoms will show the distance between the two centers in nanometers. Double clicking on a second atom will lock a line segment between those two atoms and display the distance in black. There is now another free end of the segmented line, and dragging that to any other atom will show the angle defined by the three-atom combination. Double clicking on the third atom fixes the second line segment and gives a third segment that can be dragged and double clicked to display dihedral angles. Students could, for example, explore various ring structures in this collection to determine which rings are distorted and which are not.The files that are currently used for the collection are MDL mol files, and do not contain orbital, electrostatic potential, or vibrational data. Beginning next month we will change the file format, and that information will be available to users, either through the Jmol menu (right click on any structure) or through menu choices.Not all of the molecules from the Ault paper (1) have been included, leaving room for students to model and perform calculations on many of the non-eserethole species, and to consider how modern tools of analysis might have simplified the identification of eserethole. They might also wish to determine which pair of eserethole enantiomers are the more stable. (The eserethole structures included here have all been optimized at the 6311++G (d,p) level.)
Natural Products
Molecular Models of Resveratrol  William F. Coleman
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.
Plant Chemistry |
Natural Products
Molecular Models of Lycopene and Other Carotenoids  William F. Coleman
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.
Plant Chemistry |
Natural Products
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