TIGER

Other Resources: 76 results
An Animated Interactive Overview of Molecular Symmetry  Marion E. Cass, Henry S. Rzepa, David R. Rzepa, Charlotte K. Williams
An Animated Interactive Overview of Molecular Symmetry is a series of Web pages designed to help instructors teach molecular symmetry. These pages combine interactive Jmol images and instructional text that allow students to examine and explore the operations and elements that give rise to molecular symmetry.
Crystals / Crystallography |
Group Theory / Symmetry |
Molecular Properties / Structure |
Thermodynamics
Interactive Molecular Orbitals  William F. Coleman
The majority of Introductory Chemistry texts provide students with an adequate introduction to the visual aspects of the molecular orbital model for homonuclear diatomic molecules. The treatment of heteronuclear diatomic and polyatomic molecules is less uniform. Heteronuclear diatomics, when mentioned, are invariably treated as being derived from homonuclear diatomics. While the atomic orbital energy level differences in heteronuclear diatomics is sometimes pictured, the consequences of those differences for the resultant molecular orbitals are rarely discussed. The discussion of polyatomic molecular orbitals in these texts is limited to showing that parallel p-orbitals produce delocalized pi molecular orbitals. The molecules typically mentioned in this context are benzene, nitrate ion and carbonate ion. However, It is rarely pointed out that the six p-orbitals in benzene would form 6 pi molecular orbitals, and that only one of these orbitals would look like the picture in the text.These interactive modules are designed to clarify this subject.
MO Theory
Luminescent Molecular Thermometers  William F. Coleman
The Featured Molecules this month come from the paper "Luminescent Molecular Thermometers" by Uchiyama, Prasanna de Silva, and Iwai exploring the many ways that photophysical properties can be used as temperature probes. They introduce a variety of molecule types, many of them now in our molecule collection. Excited states play a central role in this paper and it provides an opportunity to introduce students to some excited state properties.
Molecular Modeling |
Molecular Properties / Structure |
Photochemistry
Chemistry: The Molecular Science, 2nd Edition  John W. Moore, Conrad L. Stanitski, Peter C. Jurs
Finds ChemEd DL resources related to the sections of the General Chemistry textbook, Chemistry: The Molecular Science, 2nd Edition, by John W. Moore, Conrad L. Stanitski, Peter C. Jurs published by Brooks/Cole, 2005.
Chemistry: The Molecular Science, 3rd Edition  John W. Moore, Conrad L. Stanitski, Peter C. Jurs
Finds ChemEd DL resources related to the sections of the General Chemistry textbook, Chemistry: The Molecular Science, 3rd Edition, by John W. Moore, Conrad L. Stanitski, Peter C. Jurs published by Brooks/Cole, 2008.
Principles of Chemistry: The Molecular Science  John W. Moore, Conrad L. Stanitski, Peter C. Jurs
Finds ChemEd DL resources related to the sections of the General Chemistry textbook, Principles of Chemistry: The Molecular Science, by John W. Moore, Conrad L. Stanitski, Peter C. Jurs published by Brooks/Cole, 2009.
Heteronuclear Diatomic Molecular Orbital Formation  William F. Coleman
Here is a set of movies that demonstrates heteronuclear diatomic molecular orbital formation. The orbitals start at a distance where there is little or no interatomic interaction and move to the appropriate bond distance. Orbital phase is shown by the different colors.
Covalent Bonding |
MO Theory |
Enrichment / Review Materials
Nanoscale Molecular Tweezers  William F. Coleman
The featured molecules for this month are drawn from the "Research Advances" column by Angela G. King, and represent some of the structures from the research on molecular tweezers (published in J. Am. Chem. Soc. 2004, 126, 8124). The structures below are based on the figure on page 1690 showing two types of receptors that switch between U and W shapes upon coordination of soft metal cations, acting in the manner of mechanical tweezers. When viewing these molecules in Chime you must render in ball and stick or space filling modes in order to see the incorporated metal ions. In several cases the torsion angles connecting the anthracene substituents to the rest of the molecule are not well defined and have been drawn as either coplanar or orthogonal to the central ring system. At a moderate level of theory, the torsion angle in those instances where it has been set to 90° displays a broad minimum ranging for 50?130°.
Nanotechnology
Interactive Molecular Orbital Diagrams  William F. Coleman
Here is an application for constructing the molecular orbital electron configurations of heteronuclear diatomic molecules. Energy level diagrams are given for the two different cases encountered in heteronuclear diatomics of the first short period (Li2 - Ne2). This is a useful tool for having students explore questions of bond order, magnetic properties and numbers of unpaired electrons.
Covalent Bonding |
MO Theory |
Enrichment / Review Materials
3D Molecular Symmetry Shockwave; A Web Application for Interactive Visualization  Nickolas D. Charistos, Constantinos A. Tsipis, Michail P. Sigalas
3D Molecular Symmetry Shockwave is a Web-based application for interactive visualization and three-dimensional perception of molecular symmetry. The user interface is simple, and students learn how to use the program from the built-in help screens. The animation uses the Macromedia Shockwave browser plug-in, and requires a download of only 256 KB, allowing it to be used even with low bandwidth Internet connections. Its performance is comparable to a desktop application.
Crystals / Crystallography |
Group Theory / Symmetry |
Molecular Properties / Structure |
Thermodynamics
Chemistry in Focus: A Molecular View of Our World  Nivaldo J. Tro
Finds ChemEd DL resources related to the sections of the General Chemistry textbook, Chemistry in Focus: A Molecular View of Our World, by Nivaldo J. Tro published by Brooks/Cole, 2009.
Molecular Models of Plant Hormones  William F. Coleman
The paper "Synthesis of Plant Auxin Derivatives and Their Effects on Ceratopteris richardii" by Corey E. Stilts and Roxanne Fisher describing an experiment begun in the organic labs and completed in a biochemistry cell biology lab provides the featured molecules for this month. The molecules in Figure 1 of that paper have been added to the collection. There is nothing particularly surprising about their structures, but students might be interested in seeing whether they can determine any structure/regulating effect relationships as the number of synthesized auxin derivatives grows. Additionally, students with little or no biochemistry background might wish to explore other systems that act as growth regulating hormones in plants, as an introduction to the variety of molecular structures that can display such bioactivity. Such molecules range from the very simple, ethene, to the adenine-derived cytokinins (an example of which, zealtin, is shown here) and the brassinosteroids. Brassinolide, a commonly occurring brassin, is also shown. These latter two structures have also been added to the molecule collection. All of the structures have been optimized at the HF/6-31G(d) level.
Synthesis |
Biological Cells |
Hormones |
Bioorganic Chemistry
Molecular Model of Creatine Synthesis  William F. Coleman
The featured molecules for this month come from the paper Creatine Synthesis: An Undergraduate Organic Chemistry Laboratory Experiment by Andri Smith and Paula Tan on the synthesis of creatine in introductory organic chemistry. This synthesis is sufficiently straightforward to be used in non-majors and general chemistry courses. The structures illustrate some of the limitations associated with the computation of molecular structure. The two adenosine phosphates ADP and ATP exhibit a large number of conformations due to rotation of the adenine system around the bond to the ribose ring, multiple rotational conformations in the phosphate groups, the ionic state of the compound, and the interaction with the solvent or another species such as creatine. The structures that are given for ADP and ATP are derived from PM3MM calculations and are very similar to those derived using the UFF force field. Sarcosine, creatine, and creatine phosphate were treated using the model chemistry B3LYP/6-31+G(d). Perhaps the most interesting structural feature is found in the small molecule cyanamide. Observant students might notice in the Web-based structure that the NCN grouping in cyanamide is non-linear, with an angle of about 177°. This is found for essentially all levels of theory we examined up through the G2 combined model. For students who do notice this deviation from linearity it is useful to ask them whether they are surprised, ask them to defend their answer, send them to the literature to see whether such behavior is seen for cyanamide in other phases (it is), and finally to speculate on possible explanations for the observed non-linearity.
Molecular Modeling |
Molecular Properties / Structure
Molecular Models of Rosmarinic Acid and DPPH  William F. Coleman
The paper by Canelas and da Costa (1) introduces students to the antioxidant rosmarinic acid, and its interaction with the free radical DPPH. Those two molecules are the featured species this month. The original paper shows the 2-dimensional structure of the cis isomer of rosmarinic acid, although the trans isomer exhibits very similar antioxidant properties. Calculations at the DFT/B3LYP 631-G(d) level show that the trans isomer is more stable than the cis isomer in the gas phase, a situation that is expected to carry over into solution. Many antioxidants are phenols, and rosmarinic acid has four such groups available for radical formation. A DFT study by Cao et al. (2) examines the relative stabilities of the radicals formed from loss of each of the phenolic hydrogens. That paper focuses on the trans isomer, and a useful student project would be to repeat the calculations with the cis isomer. An HPLC separation of the isomers of rosmarinic acid has been published (3), and might well lead to an extension of the experiment described in ref 1 in which relative antioxidant efficiencies of the two isomers could be evaluated. DPPH has been used extensively as a standard for determining antioxidant activity. An examination of the molecular orbital occupied by the lone electron shows significant delocalization, providing a partial explanation for the stability of the neutral radical. Our gas phase structure for DPPH, also at the DFT/B3LYP 631-G(d) level, is quite consistent with several crystal structures on DPPH and DPPH in the presence of another species (4).
Natural Products
Molecular Models of Compounds in Lightsticks  William F. Coleman
The article Glowmatography, by Thomas S. Kuntzleman, Anna E. Comfort, and Bruce W. Baldwin, is the source of this month's Featured Molecules (1). Three molecules from the paper have been added to the collection and several rhodamine derivatives were featured in the November 2007 column (2).The energy transfer agent in the lightsticks is 1,2-dioxetanedione, a cyclic peroxide and high energy dimer of carbon dioxide. Students at all levels would be interested to learn that the chemistry of a toy can be used in a wide variety of applications. For example, 1,2-dioxetanedione embedded in nanoparticles has recently been used to image hydrogen peroxide in cells (3).A number of polyaromatic compounds are included in Table 1 of the source paper (1). Rubrene, 5,6,11,12-tetraphenyl-naphthacene, when optimized at the PM3 level, shows an interesting chiral twist to the napthacene backbone of about 37°. We find that twist to be present, but reduced to about 10° at the HF/6-31G(d) level, and a similar magnitude at the B3LYP/6-31G(d) level. A more complete DFT study is underway as our results do not agree with those of Käfer and Witte who find a somewhat larger twist angle (4). Those authors point out that the crystal structure of rubrene shows no twist. Rubrene also has many uses other than entertainment. It is an organic semiconductor used in LEDs, solar cells, and transistors, and has recently been shown to produce interesting self-assemblies on metal surfaces (5).Another polyaromatic compound, 5,12-bis(phenylethynyl)naphthacene, shows the expected planar structure and the molecular orbitals are consistent with a high degree of delocalization. This compound has been used to activate the bleaches in commercial teeth-whitening products (6).Other molecules from Table 1 (1) would provide students the qualitative experience of leaning about applications beyond the lightstick and the quantitative experience of optimizing structures to explore the ways in which the various substituents pack around the polycene backbone.
Molecular Modeling
Molecular Models of Polymers Used in Sports Equipment  William F. Coleman
In keeping with the 2008 National Chemistry Week theme of Having a Ball with Chemistry, the Featured Molecules this month are a number of monomers and their associated polymers taken from a paper by Sandy Van Natta and John P. Williams on polymers used in making equipment for a variety of high-impact sports (1). The molecules provide students with an introduction to an important area of applied chemistry and also enable them to examine complex structures using the models they have seen applied to small molecules.It is certainly instructive for students to build small polymer fragments using molecular model kits. Holding a model of n-decane, for example, and twisting it in various ways, provides real insight into the multiplicity of conformations available to supermolecules of polyethylene. Computer-based 3-dimensional structure drawing and visualization programs make it possible to construct large oligomers of known polymers and to begin to explore structural properties of new systems. Two such programs, free for academic use, are DSVisualizer and ArgusLab (2). DSVisualizer includes a useful set of tools for building and viewing structures and a clean geometry option that applies a Dreiding-like force field. ArgusLab adds the ability to perform both molecular mechanics and semi-empirical geometry optimization and to display various molecular surfaces. Using ArgusLab, or a similar program, students can explore the relative energies of various conformations of the substances they have built electronically. Students who are being introduced to molecular modeling and the use of more sophisticated software can easily explore the effects of the modeling and convergence parameters on the stable structures that are found, and can begin to explore the difference between global and local minima on a molecular potential energy surface. Using the conformational search program in HyperChem 7.5 on a tetramer of vinyl chloride (terminated with H; of SRRS stereochemistry; only CCCC torsions varied), approximately half of the 500 structures examined fell within 6 kcal/mol of the lowest energy structure (3). This number would increase significantly if other torsion angles were included.The use of computational software allows us to introduce students in introductory chemistry to the idea of multiple conformations, which is so important in biochemistry and much of organic chemistry. In teaching ideas behind conformational stability care should be taken when attributing conformational stability solely to non-bonded repulsions between peripheral atoms on adjacent carbon atoms. Weinhold and co-workers have recently presented strong evidence that the stability of the staggered conformer of ethane relative to the eclipsed form arises from more favorable interactions of C-H sigma bonding orbitals on adjacent carbons (4). The multiplicity of such interactions could well be responsible for conformational stability in more complex systems. Any discussion of conformational stability should also introduce students to the ultimate conformational problem, the folding of proteins and to the Folding@home project (5).
Polymerization |
Applications of Chemistry
Molecular Models of EDTA and Other Chelating Agents  William F. Coleman
Deirdre Bell-Oudry presents a variation on an old theme in her paper on using an indirect EDTA titration for sulfate analysis (1). EDTA and (often loosely) related species are this month's Featured Molecules.EDTA is a hexaprotic acid (H6Y2+) having the pKa values given in the featured paper (1). Figure 1 shows a distribution diagram for the EDTA system (2). At the pH of normal waters, the predominant species have one or both of the nitrogen atoms protonated.Complexation, however, requires that both nitrogens be deprotonated and it is generally assumed that the form that complexes with metal ions is Y4−. Structures of several forms of EDTA are included in the molecule collection (Figure 2). These structures are quite flexible having many conformations that are readily accessible at room temperature.An introduction to EDTA chemistry leads to broader questions of metal ion chelation or sequestration. Related chelating agents included in the molecule collection are EGTA, DCTA, NTA, BAPTA, and DTPA. Molecular dynamics and Hartree-Fock calculations on BAPTA (Figure 2) confirm that many conformations, ranging from those with the phenyl rings parallel to one another, to more elongated forms, are essentially isoenergetic in room temperature aqueous solution (3).Also included in the molecule collection are several crown ethers, an isophore (nonactin), and a cryptand. These not only provide students with a glimpse of the types of molecules being employed for metal ion sequestration but open a wide range of topics of current research in a variety of areas of inorganic, industrial, environmental, and biological chemistry.
Aqueous Solution Chemistry
Molecular Orbitals  Ed Vitz, John W. Moore
A section of ChemPrime, the Chemical Educations Digital Library's free General Chemistry textbook.
MO Theory |
Magnetic Properties
Solubility and Molecular Structure  Ed Vitz, John W. Moore
A section of ChemPrime, the Chemical Educations Digital Library's free General Chemistry textbook.
Precipitation / Solubility
Molecular Model of Zincon  William F. Coleman
The Featured Molecules this month are the tautomeric forms of the colorimetric reagent zincon, used in the paper by Maria Mar Areco, Maria dos Santos Afonso, and Erika Valdman on the bioabsorption of zinc, and by extension other metal ions, by seaweed. The structures presented have been calculated at the DFT/6-31G(d) level using the B3LYP functional. These structures represent energy minima, but not necessarily global minima. The structures could be used as an introduction to the concept of tautomerism, with students being asked to develop a definition of the term based on their observations of the difference(s) in linkage in the two forms. An intramolecular hydrogen bond is found in each structure, and introductory chemistry students could be encouraged to look for these structural features in molecules that are more complex than those typically encountered to introduce hydrogen bonding. More advanced students could use computational techniques to explore the energy differences between the two forms, and compare those differences to the ones observed between more traditional keto/enol examples.
Calorimetry / Thermochemistry |
Water / Water Chemistry |
Biological Cells
Molecular Model of Tubocurarine  William F. Coleman
Curare, the Karib name for the plant from which this molecule is derived, is used in traditional South American medicine and hunting because it is a muscle relaxant. The three papers by Brunsvold and Ostercamp (1, 2, 3) provide us with an abundance of candidates for Featured Molecules this month. All of the major compounds highlighted in the papers, and many of the intermediates in the synthetic schemes, have been added to our collection. Students should note the structural similarities of the various barbiturate species and of the steroid-based compounds, as well as the interesting proto-cage structure of curare. Careful examination of the conformation of the alkyl groups in various of the molecules, when looked at as Newman projections, should convince students that their expectations about staggering substituents on adjacent tetrahedral-like carbon atoms are met in the computations. However, they should also be aware that recent work casts some doubt on the traditional explanation for that staggering (1). Charged species are presented in the collection in ionic form, without counterions (those are given in the papers), and all species except curare and atricurium besylate (molecule 40 in the third paper) were optimized at either HF/631-G(d) or B3LYP/631-G(d). The latter two molecules were optimized using HF/STO-3.
Bioorganic Chemistry
Molecular Models of DNA  William F. Coleman
The featured molecules this month come from the paper by David T. Crouse on the X-ray determination of the structure of DNA. Given that most students are aware of the double helix, it seems appropriate to back up a little and examine the components that give rise to this structure. Accordingly, the molecule collection includes: Purine and pyrimidine, structural precursors of the four bases found in DNA: cytosine (C), thymine (T), adenine (A), and guanine (G) The four corresponding deoxyribonucleosides The four deoxyribonucleotides (the nucleoside monophosphates) A two-base-pair fragment showing the AT and GC hydrogen-bonded complements Several small 24-base-pair DNA fragments polyAT, polyGC, and a random array of bases. The DNA fragments provide a good opportunity to have students explore features of the Jmol and Chime menus. Using the Jmol menu as an example (right-click on the structure to bring up the menu) students can use the measuring tools to get an idea of the length of a complete turn in the DNA, the relative widths of the major and minor grooves, and the diameter of the helix. They can use the coloring schemes to detect the various base pair combinations, and learn to read the code for the random sequence. In Chime they can use the Shapely coloring scheme for this same purpose. Exploring other aspects of the menu will allow students to present the molecules in the various forms, including ribbon and cartoon views. In RNA, thymine is replaced by uracil, and the sugar moiety has an axial hydroxyl group on the carbon atom adjacent to the base binding site (the 2? carbon). The structures of uracil and of uridine monophosphate are included in the molecule collection. Students can use the Web to download and examine more complex DNAs using a site such as the Nucleic Acid Database at Rutgers University.
Nucleic Acids / DNA / RNA
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 DAPI  William F. Coleman
This month's Featured Molecule is DAPI (4′,6-diamidino-2-phenylindole), from the paper by Eamonn F. Healy (1). The utility of DAPI is a consequence of its being a minor-groove binder to DNA. A crystal structure of DAPI binding to the minor groove of a synthetic DNA has been determined, and the structure file made available through the RCSB Protein Data Bank (2, 3). That structure is also included in the Featured Molecules Collection, with the water molecules removed for the sake of clarity. For many students this may be their first encounter with the binding of small molecules to DNA. Another example of such binding is the intercalation of the antibiotic actinomycin into DNA. The Department of Biology at the University of Hamburg maintains an excellent Web site showing both crystal and NMR structures of actinomycin intercalation (4). Observant students will also note in the structure of DAPI a theme that has appeared several times in our Featured Molecules, and that is the non-planarity of adjacent delocalized ring systems. In DAPI, it is a five-membered ring adjacent to a six-membered ring, and the observed departure from planarity is less than that in biphenyl. Students might be asked to explain that difference.
Nucleic Acids / DNA / RNA
Molecular Models of Dyes  William F. Coleman
The paper on the synthesis of several dyes by James V. McCullagh and Kelly A. Daggett (1) provides us with the JCE Featured Molecules for this month. The authors mention various applications of these dyes, ranging from commercial dyeing to techniques for determining the course of complex biochemical processes. One of the reaction products, rhodamine B, is a member of a family of molecules that are widely used as tunable laser dyes. In this application, the rhodamines are most commonly encountered in a cationic form, rather than in the neutral form shown in the paper. In the cations, the carboxyl group is no longer part of a ring system. Several different members of the rhodamine family are included in the molecule collection because substituents have a marked effect on the effective lasing range of a given dye. Additionally, the solvent and the excitation source also influence the lasing range (2). Students can learn more about the relationship between structure, absorption and emission properties, and lasing ranges of various dyes by consulting ref 2 and from PhotochemCAD, Jonathan Lindsey's free application (3).
Dyes / Pigments
Molecular Models of Indicators  William F. Coleman
The article by Nicholas C. Thomas and Stephen Faulk on "Colorful Chemical Fountains" (1) reminds us that color—the colors of acid–base indicators or of metal complexes—is responsible for many of us developing an interest in chemistry. The featured molecules this month are the acid and base forms of three common indicators–phenolphthalein, methyl orange, and methyl red. These three substances display interesting structural features as the pH-induced transformation from one form to another takes place in three different ways. In the case of phenolphthalein, the lactam ring is cleaved on deprotonation to produce a carboxyl group with the concomitant removal of a proton from a phenolic group. In methyl orange, one of the nitrogen atoms is protonated in the acid form, and that proton is lost in the base form. In methyl red, a carboxylic acid function is deprotonated. There are many other interesting aspects of acid–base indicators. Since most plants and fruits contain pigments that show a color change in some pH range, it is difficult to state with any degree of certainty when these changes were first put to use in a systematic fashion. The Spanish alchemist Arnaldus de Villa Nova (Arnold of Villanova) is purported to have used litmus in the early 14th century. In general systematic use of indicators is traced to the latter half of the nineteenth century with the development of the three synthetic indicators described above. Many students will be familiar with the use of phenolphthalein to identify blood—often shown on the various forensic chemistry TV dramas by dropping some solution on a cotton swab that has been used to pick up some of the sample in question. If the swab turns red we frequently hear "It's blood". The reality of using phenolphthalein in this way is more complicated. The test is presumptive for the presence of blood, but not conclusive. It is not an acid–base reaction but rather, in the presence of hydrogen peroxide, relies on hemoglobin to catalyze the oxidation of phenolphthalein. An interesting assignment for students in a high-school or non-majors course would be to have them explore the details of this Kastle–Meyers test to see just what is involved in the correct application of the test, and what factors complicate the process. For example, would tomato juice infused with asparagus juice give a positive Kastle–Meyers test? Historically phenolphthalein was used in a variety of laxatives. Recently that usage has been discontinued due to concern about the carcinogenic nature of the substance. A review of the history of the controversy surrounding the use of phenolphthalein in laxatives would make a good research paper at the high-school level. Lastly, students with some practice building structures and performing calculations might wish to explore the structures of two other forms of phenolphthalein—one found in very acidic solutions, having an orange color, and one found in very basic solutions that is colorless.
Molecular Properties / Structure
The Molecular View of Equilibrium  Ed Vitz, John W. Moore
A section of ChemPrime, the Chemical Educations Digital Library's free General Chemistry textbook.
Equilibrium
Molecular Model for Water  Ed Vitz
A section of ChemPrime, the Chemical Educations Digital Library's free General Chemistry textbook.
Atomic Properties / Structure |
Water / Water Chemistry
Chime Library  William F. Coleman
Chime files for many molecular structures.
Molecular Properties / Structure |
Enrichment / Review Materials
Multiple Bonds and Molecular Shapes  Ed Vitz, John W. Moore
A section of ChemPrime, the Chemical Educations Digital Library's free General Chemistry textbook.
Molecular Properties / Structure
Kinetic Theory of Gases: Molecular Speeds  Ed Vitz, John W. Moore
A section of ChemPrime, the Chemical Educations Digital Library's free General Chemistry textbook.
Kinetic-Molecular Theory
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 Volatile Organic Compounds  William F. Coleman
This month's Featured Molecules come from the Report from Other Journals column, Nature: Our Atmosphere in the Year of Planet Earth, and the summary found there of the paper by Lelieveld et al. (1, 2) Added to the collection are several volatile organic compounds (VOCs) that are emitted by a variety of plants. The term VOCs is a common one in environmental chemistry, and is interpreted quite broadly, typically referring to any organic molecule with a vapor pressure sufficiently high to allow for part-per-billion levels in the atmosphere. Common VOCs include methane (the most prevalent VOC), benzene and benzene derivatives, chlorinated hydrocarbons, and many others. The source may be natural, as in the case of the plant emissions, or anthropogenic, as in the case of a molecule such as the gasoline additive methyl tert-butyl ether (MTBE).The oxidation of isoprene in the atmosphere has been a source of interest for many years. Several primary oxidation products are included in the molecule collection, although a number of isomeric forms are also possible (3).The area of VOCs provides innumerable topics for students research papers and projects at all levels of the curriculum from high-school chemistry through the undergraduate courses in chemistry and environmental science. Along the way students have the opportunity for exposure to fields such as epidemiology and toxicology, that may be new to them, but are of increasing importance in the environmental sciences. The MTBE story is an interesting one for students to discover, as it once again emphasizes the role that unintended consequences play in life. An exploration of the sources, structures, reactivity, health and environmental effects and ultimate fate of various VOCs reinforces in students minds just how interconnected the chemistry of the environment is, a lesson that bears repeating frequently.
Molecular Modeling |
Atmospheric Chemistry
Molecular Models of Candy Components  William F. Coleman
This month's Featured Molecules come from the paper "A Spoonful of C12H22O11 Makes the Chemistry Go Down: Candy Motivations in the High School Chemistry Classroom" by Fanny K Ennever on using candy to illustrate various principles. They include sucrose and the invert sugar that results from the hydrolysis of sucrose. Students should look for structural similarities between sucrose and the hydrolysis products glucose and fructose, and verify that all three are indeed hydrates of carbon. They should also inspect the models to see whether the position of the substituents in the five and six membered rings are the same in the sucrose and in the hydrolysis products. Also included are two esters important in fruit flavoring of candies. Flavor and aroma are inexorably intertwined in the taste experience and no single compound is responsible for that experience. Methyl cinnamate, included here, is one of over 100 esters, and over 300 compounds, involved in the taste of strawberries (1). Isoamyl acetate is a major component of the taste of bananas. Lastly, chocolate, perhaps nothing else need be said. There is a great deal of confusion in the popular press and on the internet between theobromine, found in cocoa beans, and caffeine. Both molecules are included here and students should easily see why the two might be confused. Consequently there are many exaggerated claims about caffeine in chocolate. An interesting assignment would be for teams of students to find reliable data on the physiological effects of these similar molecules, and to find good analyses on the actual level of caffeine in cocoa beans, versus the amount added in the candy production process, if any.
Consumer Chemistry |
Molecular Modeling
Molecular Models of Compounds in Maple Syrup  William F. Coleman
This month's issue of J. Chem. Educ. includes articles by David Ball dealing with the chemical composition of honey (1) and maple syrup (2). The JCE Featured Molecules for this month are drawn from those papers. In prior months we have included sucrose, glucose, and fructose (3), and all of the naturally occurring amino acids (4) in the molecule collection. This month we add the molecules identified in Table 4 of ref 2 as probable contributors to the taste of maple syrup. This group of molecules could serve easily as a starting point for a variety of student activities in the area of taste. Students in non-majors courses could be asked to identify structural similarities and differences among the various molecules and could be introduced to functional groups. Students could look for other foods in which some of these molecules are found, and could begin to develop a list of molecules contributing to flavor. In the penultimate paragraph of the maple syrup paper there is a list of substances used as flavoring agents in artificial (maple) syrup. What molecules are in fenugreek and lovage that might be important in flavoring? What are the structures of the other molecules in that paragraph and what, if any, structural features do they have in common with the featured molecules? Students in organic or biochemistry courses could begin to explore the chemistry of taste in more detail. Good starting points for this work are The Chemistry of Taste: Mechanisms, Behaviors, and Mimics by Peter Given and Dulce Paredes (5) and the Chemical and Engineering News Web site (6), which includes a number of articles on this subject.
Descriptive Chemistry |
Solutions / Solvents |
Food Science |
Plant Chemistry
Molecular Models of Antioxidants and Radicals  William F. Coleman
This month's featured molecules come from the paper by John M. Berger, Roshniben J. Rana, Hira Javeed, Iqra Javeed, and Sandi L. Schulien (1) describing the use of DPPH to measure antioxidant activity. DPPH was one of the featured molecules in September 2007 (2) and the basics of antioxidant activity were introduced in last month's column (3). In addition, some of the other molecules in the paper are already in the featured molecules collection (4). The remaining structures in the Figure 1 and Table 1 of the paper have been added to the collection. All structures have been optimized at the 6-311G(D,P) level. These molecules suggest a number of possible student activities, some reminiscent of previous columns and some new. (R,R,R)-α-tocopherol is one of the molecules in the mixture that goes by the name vitamin E. These molecules differ in the substituents on the benzene ring and on whether or not there are alternating double bonds in the phytyl tail. In (R,R,R)-α-tocopherol the R's refer to the three chiral carbon atoms in tail while α refers to the substituents on the ring. (R,R,R)-α-Tocopherol is the form found in nature. An interesting literature problem would be to have students learn more about the vitamin E mixture and the differing antioxidant activity of the various constituents. Additionally they could be asked to explore the difference between the word natural as used by a chemist, and "natural" as used on vitamin E supplements. Can students find regulations governing the use of the term "natural"? Can they suggest alternative legislation, and defend their ideas? If students read about vitamin C they will discover that only L-ascorbic acid is useful in the body. It would be interesting to extend the experiment described in the Berger et al. paper (1) to include D-ascorbic acid. How do the antioxidant abilities of the enantiomers, as determined by reaction with DPPH compare? Is this consistent with the behavior in the body? Why or why not? Berger et al. mention two other stable neutral radicals, TEMPO (2,2,6,6-tetramethylpiperidine-1-oxyl) and Fremy's salt. In a reversal from the use of stable radicals to measure antioxidant properties, these two molecules have proven to be very versatile oxidation catalysts in organic synthesis, and would make a rich source of research papers for students in undergraduate organic courses.
Free Radicals |
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
Molecular Models of Leaf Extracts  William F. Coleman
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.
Plant Chemistry
Molecular Models of Annatto Seed Components  William F. Coleman
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.
Plant Chemistry |
Natural Products
Molecular Models of Peroxides and Albendazoles  William F. Coleman
This month our featured molecules come from two sources, the paper by Marina Canepa Kittredge, Kevin W. Kittredge, Melissa S. Sokol, Arlyne M. Sarquis, and Laura M. Sennet on the stability of benzoyl peroxide (1) and the paper by Graciela Mahler, Danilo Davyt, Sandra Gordon, Marcelo Incerti, Ivana Núñez, Horacio Pezaroglo, Laura Scarone, Gloria Serra, Mauricio Silvera, and Eduardo Manta on the synthesis of an albendazole metabolite (2).The benzoyl peroxide paper is targeted at non-majors courses, but the molecule and related peroxides contain a number of interesting structural features that could be explored in traditional introductory and in upper-level courses. The first feature is the OO bond itself. In the three examples included in the collection the bond length computed at the B3LYP/6-311++G(d,p) level ranges from 133.8 pm for dimethyl peroxide to 144.9 pm for hydrogen peroxide. The experimental value for the latter is 147.5 pm and the Computational Chemistry Comparison and Benchmark DataBase (CCCBD) gives a wide range of computed OO bond lengths in H2O2 for more than 20 model chemistries (3).The XOOXʹ dihedral angle in these peroxides also shows interesting properties that have been difficult to reproduce theoretically. In hydrogen peroxide the experimental value is 119.8°, while our calculation gives 121.5°. Again the CCCBD reports a wide variation in this angle, including methods that produce a value of 180°. On the other hand, our model of benzoyl peroxide has a dihedral angle of 86.6°, and dimethyl peroxide shows a dihedral angle of 180°. Weinhold and Landis discuss the angle in hydrogen peroxide in terms of a stabilization of the gauche form through an nσ* interaction between oxygen lone pairs and empty CO σ* orbitals (4). Many levels of theory produce 180° dihedral angles for dimethyl peroxide and, as Tonmunphean, Parasuk, and Karpfen have pointed out, minima in the 120° range are not observed until coupled-cluster models are applied (5). The accepted experimental structure with a 119 ± 10° dihedral angle comes from an electron diffraction study (6). These experimental and high-level theoretical calculations lead us to conclude that the model proposed by Weinhold and Landis applies to more complex peroxides as well as to H2O2.In the case of albendazole and the oxygenated albendazoles, it is interesting to monitor the computed charges on the sulfur atoms with oxygenation. The charges on the sulfur atoms, computed at the B3LYP/6-311++G(d,p) level, are 0.066, 0.768 and 1.123 for 0, 1 and 2 oxygens on the sulfur atom respectively. Students could be asked to predict and explain the order of the charges, and to comment on how the charges inform the description of bonding about the sulfur atom. To what extent is the hypervalent species ionic? Does this influence how we should think of d-orbital participation in such molecules?
Molecular Modeling
Solubility and Molecular Structure in the Environment  Sarah Yue
A section of ChemPrime, the Chemical Educations Digital Library's free General Chemistry textbook.
Precipitation / Solubility
Spontaneous Processes and Molecular Probability  Ed Vitz, John W. Moore
A section of ChemPrime, the Chemical Educations Digital Library's free General Chemistry textbook.
Reactions
Dependence of S on Molecular Structure  Ed Vitz, John W. Moore
A section of ChemPrime, the Chemical Educations Digital Library's free General Chemistry textbook.
Molecular Mechanics / Dynamics
Molecular Gastronomy; Cooking in a Vacuum  Ed Vitz
A section of ChemPrime, the Chemical Educations Digital Library's free General Chemistry textbook.
Molecular Properties / Structure
Kinetic Theory of Gases: The Total Molecular Kinetic Energy  Ed Vitz, John W. Moore
A section of ChemPrime, the Chemical Educations Digital Library's free General Chemistry textbook.
Kinetic-Molecular Theory
Kinetic Theory of Gases: The Distribution of Molecular Speeds  Ed Vitz, John W. Moore
A section of ChemPrime, the Chemical Educations Digital Library's free General Chemistry textbook.
Kinetic-Molecular Theory
Molecular Models of Components in Red Bull Energy Drinks  William F. Coleman
Our featured molecules for this month come from the paper by André J. Simpson, Azadeh Shirzadi, Timothy E. Burrow, Andrew P. Dicks, Brent Lefebvre, and Tricia Corrin (1). In the article, the authors describe the use of NMR to identify and quantify a number of components in the energy drink Red Bull, in both regular and sugar-free forms. Some of these substances glucose, sucrose, caffeine, and methylcobalamin (vitamin B12) are already in the JCE Featured Molecules collection, and we add twelve additional structures this month (2).Aspartame is the name for an artificial, non-saccharide sweetener, marketed under a number of trademark names, including Equal, NutraSweet, and Canderel.Although the NMR experiment is designed for upper-level undergraduates, Red Bull and energy drinks in general as well as several of the components of Red Bull offer interesting possibilities for study across the curriculum, starting at the pre-college level. The drink itself and component species including taurine, aspartame, and the potassium salt of acesulfame (often referred to as acesulfame potassium in that reverse nomenclature used by the drug industry) have a life of their own in the internet world of pseudo-science and urban legend. It is never too soon to begin to help students learn to navigate the pot-hole filled road that is the information highway. A discussion might begin with a simple question, What have you heard about Red Bull? or What have you heard about aspartame?. One could then proceed to explore the claims made about the health effects of these substances, and move in the direction of finding reliable information to support or refute these claims. As much as we might like our students to rely solely on the primary chemical literature as their source of chemical information, the fact is that the Internet is where almost all of them go first when researching a new topic. Of course, that is true of most of us as well, but we have the tools to separate wheat from chaff, and the majority of our students do not. If we don't ask our students how they analyze information, we will never know what myths they continue to believe. This was recently illustrated for me in dramatic fashion when an astrophysicist colleague told me that despite his very best efforts, a number of his students in introductory astronomy still clung to doubts about moon landings.The featured molecules this month suggest other activities. Students in introductory or analytical chemistry could be asked to measure the pH of various drinks containing citric acid or citrate ion, and to then calculate the distribution of the various citrate species at that pH. It would also be instructive to have students consider why the pKa values for citric acid (3.1, 4.8, and 6.4) are more closely spaced than those for phosphoric acid. The inositol structure that is included here is the myo-inositol isomer. Students in organic or physical chemistry could model structures of other isomers and compare their energies to this predominant form. The sulfur-oxygen bond in the acesulfame anion is quite long (177 pm) when computed using density functional theory, the B3LYP functional and a 6-31G(d,p) basis set. An interesting question would be whether or not this bond remains unusually long in other compounds where the oxygen is also part of a ring system.
Molecular Modeling
Molecular Model of trans-3-(9-Anthryl)-2-Propenoic Acid Ethyl Ester  William F. Coleman
The Featured Molecules this month come from the paper by Nguyen and Weisman on solvent-free Wittig reactions and the stereochemical consequences of crowding in the transition state. The molecules include those pictured in the paper as well as the cis-isomer of 3-(9-anthryl)-2-propenoic acid ethyl ester. All structures were optimized at the B3LPY/6-31G* level. In the case of ethyl cinnamate, the cis-isomer is slightly more stable thermodynamically than the trans isomer, lending further support for the argument that the observed product distribution arises from the energetics of the transition state.
Molecular Modeling |
Molecular Modeling |
Molecular Mechanics / Dynamics
Molecular Models of Ruthenium(II) Organometallic Complexes  William F. Coleman
The featured molecules for this month come from the paper "Experiments in Thermodynamics and Kinetics of Phosphine Substitution in (p-Cymene)RuCl2(PR3)" by Ozerov, Moura, and Hoffman in which they study the reactions of a number of "piano stool" complexes of ruthenium(II). The synthesis of compound 2a offers students an alternative to the preparation of ferrocene if they are only preparing one metal-arene complex, and the use of the (p-cymene)RuCl2 dimer as a starting material introduces them to a compound that has become important for the synthesis of a number of ruthenium catalysts. Two structures are found for the dimer in the gas phase, one with the chlorides cis to one another and a more stable form with the chlorides trans. DFT calculations using the LanL2MB basis set and the B3LYP functional in Gaussian 03 (1) show the trans form to be about 90 kJ/mol more stable than the cis form. The structures of the trans form of the dimer and of compound 2a are presented in 2 formats with bonds from the ruthenium ion to all of the carbons in the aryl ring and with a single line to a ghost atom in the center of the ring. These are the two common ways of representing such structures but students should be made aware that the overall coordination about the ruthenium in both the dimer and in compound 2a is octahedral, and should look at the structures to convince themselves of that fact. It is also instructive to look at compound 2a, and the other piano stool complexes that are made in the paper, to see how deceptive representation of the triphenylphosphine moiety as PR3 is in terms of the stereochemical bulk of that group.
Organometallics
Collection of Chiral Drug, Pesticide, and Fragrance Molecular Models  William F. Coleman
The article by Mannschreck, Kiessewetter, and von Angerer on the differential interactions between enantiomers and biological receptors (1) is the source for this month's Featured Molecules. Included in the molecule collection are all of the molecules described in the paper. In many instances we have included structures of multiple optical isomers of the same molecule so that students can not only see the forms that are active, but those that are less active, inactive, or act in an undesirable manner. These molecules will serve as good practice in determining optical configurations, and will also introduce additional forms of isomerism that students may be less familiar with than they are with R and S. Since multiple enantiomers and diastereomers are provided, students may use these molecules, together with an appropriate computational package, to verify that enantiomers have the same energy while diastereomers do not. The tuberculosis drug ethambutol provides an interesting case as both nitrogen atoms are also chiral as well as the two chiral carbon atoms. A calculation on a given structure will include the effect of that nitrogen chirality, although nitrogen inversion is expected to be quite rapid in this molecule. The conformations for the ethambutol molecules that are included here consider all four chiral atoms and are of the form (CNNC). A reasonable computational exercise would be to find the transition state for nitrogen inversion and the barrier height for that process. The supplemental material that is included with the featured article (1) includes a number of molecules that we will add to the collection as time permits. The result, including enantiomers and diastereomers, will be well over 200 additional molecules. A notice will appear in the JCE Featured Molecules column when this new set of molecules is available in JCE Online.
Chirality / Optical Activity |
Biosignaling
Molecular Models of Products and Reactants from Suzuki and Heck Syntheses  William F. Coleman
Our Featured Molecules this month come from the paper by Evangelos Aktoudianakis, Elton Chan, Amanda R. Edward, Isabel Jarosz, Vicki Lee, Leo Mui, Sonya S. Thatipamala, and Andrew P. Dicks (1), in which they describe the synthesis of 4-phenylphenol using an aqueous-based Suzuki reaction. The authors describe the various ways in which this reaction addresses concerns of green chemistry, and point out that their product bears structural similarity to two non-steroidal anti-inflammatory drugs (NSAIDs), felbinac and diflunisal. A number of molecules from this paper and its online supplemental material have been added to the Featured Molecules collection. Students will first notice that the aromatic rings in the molecules based on a biphenyl backbone are non-planar, as is the case in biphenyl. If they look carefully at diflunisal, they will notice that the carbon atoms are in a different chemical environment. One way in which to see the effect of these differing environments is to examine the effect of atom charge on the energies of the carbon 1s orbitals. Figure 1 shows this effect using charges and energies from an HF/631-G(d) calculation. A reasonable question to ask students would be to assign each of the data points to the appropriate carbon atom. As an extension of this exercise students could produce similar plots using different computational schemes. Are the results the same; are they parallel. This would be a useful problem when dealing with the tricky question of exactly what is meant by atom charge in electronic structure calculations. Students with more expertise in organic chemistry could explore extending the synthesis of 4-phenylphenol to produce more complex bi- and polyphenyl-based drugs. This may well be the first time that they have seen coupling reactions such as the Suzuki and Heck reactions. Students in introductory and non-science-major courses might well find the NSAIDs to be an interesting group of molecules, and could be asked to find information on the variety of molecules that display the anti-inflammatory properties associated with NSAIDs. Do they find structural similarities? Are there various classes of NSAIDs? Are they familiar with any of these molecules? Have they taken any NSAIDs? If so, for what reason? Is there any controversy about any of the NSAIDs? As with all of the molecules in the Featured Molecules collections, those added this month provide us with a number of ways of showing students the practical relevance of what they sometime see only as lines on a page. Molecules do matter.
Synthesis
The Visible and Ultraviolet Spectra of Molecules: Molecular Orbitals  Ed Vitz, John W. Moore
A section of ChemPrime, the Chemical Educations Digital Library's free General Chemistry textbook.
UV-Vis Spectroscopy
Molecular Gastronomy and the Color of Cooked Green Beans  Ed Vitz
A section of ChemPrime, the Chemical Educations Digital Library's free General Chemistry textbook.
Atomic Properties / Structure
Molecular Models of Real and Mock Illicit Drugs from a Forensic Chemistry Activity  William F. Coleman
The Featured Molecules for this month come from the paper by Shawn Hasan, Deborah Bromfield-Lee, Maria T. Oliver-Hoyo, and Jose A. Cintron-Maldonado (1). The authors describe a forensic chemistry exercise in which model compounds are used to simulate the behavior of various drugs in a series of chemical tests. Structures of a number of the chemicals used in the experiment, and several of the drugs they are serving as proxy for, have been added to the molecule collection. Other substances used in the experiment are already part of the collection, including caffeine and aspirin. One structure that may be both intriguing and confusing to students is that of chlorpromazine (Thorazine, Figure 1). A majority of students might well expect the ring portion of the molecule to show a planar structure. This is not what is found from calculations at the HF/6311++G(d,p) level in both the gas phase and in water. Instead, the three rings are in a V-like formation with a deformation of approximately 50 degrees from planarity. Tracking down the source of this non-planarity would be a useful computational exercise. Does it arise from the presence of the alkyl chain (steric effect), from the chloro group (electronic effect), or from electronic effects involving the elements of the heterocyclic ring? As a starting point to addressing these questions, students could be introduced to the use of model compounds in computation. One such compound would be the parent ring system phenothiazine (Figure 2). That molecule contains neither a chloro substituent nor an extended alkyl group. Is it also found to be non-planar? Is the deformation angle the same, larger, or smaller than in chlorpromazine? Does the addition of chloro group to phenothiazene change the angle significantly? What about the addition of an alkyl group? If the model compound is forced to be planar are all of the vibrational frequencies real (positive)? If not, what type of deformation is suggested by the imaginary (negative) vibration?
Drugs / Pharmaceuticals |
Forensic Chemistry
Molecular Models of Reactants and Products from an Asymmetric Synthesis of a Chiral Carboxylic Acid  William F. Coleman
Our JCE Featured Molecules for this month come from the paper by Thomas E. Smith, David P. Richardson, George A. Truran, Katherine Belecki, and Megumi Onishi (1). The authors describe the use of a chiral auxiliary, 4-benzyl-2-oxazolidinone, in the synthesis of a chiral carboxylic acid. The majority of the molecules used in the experiment, together with several of the pharmaceuticals mentioned in the paper, have been added to our molecule collection. In many instances multiple enantiomeric and diastereomeric forms of the molecules have been included. This experiment could easily be extended to incorporate various aspects of computation for use in an advanced organic or integrated laboratory. Here are some possible exercises using the R and S forms of the 4-benzyl-2-oxazolidinone as the authors point out that both forms are available commercially. Calculation of the optimized structures and energies of the enantiomers at the HF/631-G(d) level using Gaussian03 (2) produces the results shown in Table 1. Evaluation of the vibrational frequencies results in no imaginary frequencies and the 66 real frequencies are identical for the two forms. Examination of the computed IR spectra also shows them to be identical. Additionally, the Raman and NMR spectra can be calculated for the enantiomers and compared to experimental values and spectral patterns. A tool that is becoming increasingly important for assigning absolute configuration is vibrational circular dichroism (VCD). Although the vibrational spectra of an enantiomeric pair are identical, the VCD spectra show opposite signs, as shown in Figure 1. One can imagine a synthesis, using an unknown enantiomer of the chiral auxiliary, followed by calculations of the electronic and vibrational properties of all of the intermediates and the product, and determination of absolute configuration of reactants and products by comparison of experimental and computed VCD spectra. Using a viewer capable of displaying two molecules that can be moved independently, students could more easily visualize the origin of the enantiomeric preference in the reaction between the chelated enolate and allyl iodide.
Green Chemistry
Inorganic Molecules; A Visual Database  Charles E. Ophardt, Evan M. Davis, Dustin Underwood
Inorganic Molecules: A Visual Data Base contains text and graphics describing 66 molecules and ions commonly used as examples in general chemistry courses. For each molecule, fifteen molecular properties are presented visually by eight or nine different molecular models created by the CAChe Scientific Molecular Modeling program.
Atomic Properties / Structure |
MO Theory |
Molecular Properties / Structure
SymmetryApp; An Interactive Computer Program To Help Students Learn Molecular Symmetry Elements and Operations  Andrew L. Sargent, David E. Meyer
SymmetryApp is a new visualization program characterized by a high level of user interactivity. Specifically, it is able to define a symmetry element anywhere in the molecule and determine the effect of the corresponding symmetry operation. This allows students to capitalize on the most important aspect of interactive learning?to make mistakes and to learn from them.
Group Theory / Symmetry
Hückel Determinant Solver  Robert M. Hanson
Generates energy diagrams for simple Hückel molecular orbital systems using JavaScript. You can specify the determinant or select one for a specific compound from a list.
Computational Chemistry |
MO Theory |
Theoretical Chemistry |
Enrichment / Review Materials
Antiandrogen Prostate Cancer Drugs  William F. Coleman
These interactive images are linked to molecular structures or other graphic images from articles in our print Journal. Many articles in the Journal of Chemical Education include molecular structures naturally in a two-dimensional representation. This collection of interactive Chime-based structures are chosen from some of these molecules. While many such Web-based structure collections exist, having the structures in a single location and linked to specific articles in JCE (and vice versa) will benefit both teachers and students.
Molecular Modeling |
Molecular Properties / Structure
Intermolecular Forces (Netorials)  Rachel Bain, Mithra Biekmohamadi, Liana Lamont, Mike Miller, Rebecca Ottosen, John Todd, and David Shaw
Intermolecular Forces: this is a resource in the collection "Netorials". In this resource there is a review of Lewis structures, molecular geometry, electronegativity, or molecular polarity. After that, you can learn about the forces of attraction that exist between molecules. This module explores London forces and dipole-dipole forces (including hydrogen bonds). The Netorials cover selected topics in first-year chemistry including: Chemical Reactions, Stoichiometry, Thermodynamics, Intermolecular Forces, Acids & Bases, Biomolecules, and Electrochemistry.
Noncovalent Interactions
Penicillin and Vitamin B12  William F. Coleman
The WebWare Molecules for July are mentioned in the article "The History of Molecular Structure Determination Viewed through the Nobel Prizes", by Jensen, Palenik, and Suh. One of the recipients discussed, Dorothy Crowfoot Hodgkin, won the Nobel Prize in Chemistry in part for determining the structures of penicillin and vitamin B12.
Molecular Modeling |
Molecular Properties / Structure
JCE Featured Molecules  William F. Coleman, Randall J. Wildman
These interactive images are linked to molecular structures or other graphic images from articles in our print Journal. Many articles in the Journal of Chemical Education include molecular structures naturally in a two-dimensional representation. This collection of interactive Chime-based structures are chosen from some of these molecules. While many such Web-based structure collections exist, having the structures in a single location and linked to specific articles in JCE (and vice versa) will benefit both teachers and students. In addition to static images, two fully manipulable versions (Jmol, MDL Chime) of these molecules are available.
Molecular Modeling |
Molecular Properties / Structure |
Enrichment / Review Materials
Quantum States of Atoms and Molecules  Theresa Julia Zielinski, Erica Harvey, Robert Sweeney, David M. Hanson
Quantum States of Atoms and Molecules is an introduction to quantum mechanics as it relates to spectroscopy, the electronic structure of atoms and molecules, and molecular properties. A digital, living textbook, it provides opportunities not found in conventional textbooks opportunities that allow students to develop skills in information processing, critical thinking or analytical reasoning, and problem solving that are so important for success.
Quantum Chemistry
The Effect of Anharmonicity on Diatomic Vibration; A Spreadsheet Simulation  William F. Coleman, Kieran F. Lim
Instructors and students can use this spreadsheet to quickly and easily observe how the shape of a one-dimensional vibrational potential energy curve and its associated vibrational quantum energy levels depend on the anharmonicity. This illustrates the connection between the harmonic (approximation) and anharmonic descriptions of molecular vibrations.
IR Spectroscopy |
Enrichment / Review Materials
Sulfur dichloride, SCl2  William F. Coleman, Randall J. Wildman
This month's molecule is sulfur dichloride, SCl2. This and other small inorganic molecules are discussed in the article by Matta and Gillespie. They describe electron density in molecules and how to analyze it to obtain information about molecular bonding and structure. Different depictions of electron density in SCl2 and other small molecules emphasize different aspects of their electron density and of the structures of the molecules.
Molecular Properties / Structure
Featured Molecule Sample Web Page  William F. Coleman, Randall J. Wildman
Over the next few months we will be announcing some new and exciting additions to the scope of JCE WebWare, our online feature that publishes Web-based materials for chemical education. One such addition is providing interactive images available at the JCE WebWare site that are linked to molecular structures or other graphic images of articles printed in this Journal. As an example, a significant fraction of articles in the Journal of Chemical Education include one or more molecular structures naturally in a two-dimensional representation. We would like to build a collection of interactive Chime-based structures for some of these molecules. While many such structures exist in other Web-based collections, having them in one location and linked to a specific article in JCE will greatly benefit both teachers and students. Below is an example of such a collection, derived from a paper in C & E News. Many students have difficulty "seeing" molecules in three dimensions and linking two-dimensional with three-dimensional representations of molecular structures. The more they practice doing so, the more skilled they will become. Additionally, as we try to teach students to draw "form/function" conclusions about molecular behavior, "seeing" the three-dimensional structure is crucial.
Molecular Modeling
ChemPaths 104 M Feb 14  John W. Moore
Today in Chem 104: * Lecture: Review for Exam I (email questions or topics for discussion during the review session to Prof. Moore by 9am today) * No assigned reading for today. * Exam I on Wednesday Feb 16: Covers material through Feb 11; Biomolecules tutorials, Molecular Structure, Aspirin, and Biodiesel Labs.
Bioorganic Chemistry
Restricted Hartree-Fock SCF Calculations Using Microsoft Excel  Mark A. Freitag, Cortney A. Boots, Taylor R. Page
Courses in computational chemistry are increasingly common at the undergraduate level. Excellent user-friendly programs, which make the execution of ab initio calculations quite simple, are available. However, there is a danger that the underlying SCF procedure (usually coupled with contracted Gaussian atomic orbital basis sets) can become a ?black box? for the student. This Microsoft Excel spreadsheet contains all the essential elements of far more complicated ab initio calculations, but on the simplest possible molecular system.
Computational Chemistry |
Mathematics / Symbolic Mathematics |
MO Theory |
Quantum Chemistry |
Theoretical Chemistry
3D NormalModes Shockwave; A Web Application for Interactive Visualization and Three Dimensional Perc  Nickolas D. Charistos, C. A. Tsipis, Michael P. Sigalas
3D Normal Modes is a Web application for interactive visualization and three-dimensional perception of the normal modes of molecular vibration, suitable for undergraduate students in chemistry. The application uses the Macromedia Shockwave plug-in and has been designed and developed especially for the Web. It has a simple graphical user interface and requires a download of only 120 KB, allowing it to be used even with low bandwidth Internet connections. Its performance is comparable to a desktop application.
IR Spectroscopy |
Raman Spectroscopy
Acids and Bases (Netorials)  Rachel Bain, Mithra Biekmohamadi, Liana Lamont, Mike Miller, Rebecca Ottosen, John Todd, and David Shaw
Acids and Bases: this is a resource in the collection "Netorials". In this module there is an introduction to the chemical properties of acids and bases. Afterwards, the sections include topics such as Molecular Structures of Acids and Bases, Ionization constants, properties of salts, buffers and Lewis theory of Acids and Bases. The Netorials cover selected topics in first-year chemistry including: Chemical Reactions, Stoichiometry, Thermodynamics, Intermolecular Forces, Acids & Bases, Biomolecules, and Electrochemistry.
Acids / Bases
Organic Xenobiotics  William F. Coleman
The molecules for this month come from the article, Intermolecular Forces as a Key to Understanding the Environmental Fate of Organic Xenobiotics, by Ryan E. Casey and Faith A. Pittman. The paper describes an interesting approach to introducing students in an environmental science course, with no required chemistry background, to important questions of the ways in which molecular geometry and polarity affect the behavior of organic molecules in the environment.
Molecular Properties / Structure
Electrostatics Attraction (GCMP)  David M. Whisnant
Electrostatics Attraction: this is a resource in the collection "General Chemistry Multimedia Problems". In this problem we will correlate molecular polarity with the attraction of liquids to a charged rod. General Chemistry Multimedia Problems ask students questions about experiments they see presented using videos and images. The questions asked apply concepts from different parts of an introductory course, encouraging students to decompartmentalize the material.
Noncovalent Interactions
ChemPaths 104 M Feb 7  John W. Moore
Today in Chem 104: Lecture: Biochemistry: DNA; Importance of Molecular Structure * Reading: Kotz: Chemistry of Life (pp. 503-510); Moore:Ch. 3: Sec. 11;Ch. 12: Sec. 7 * Moodle Tutorials o DNA 1 (including debriefing) o DNA 2 (including debriefing) o DNA 1 and 2 Quiz due TODAY 11:55pm * Homework #4 due F Feb 11, 11:55 PM
Nucleic Acids / DNA / RNA
The Big Picture; A Classroom Activity for Organic Chemistry  William F. Coleman
In the article "The Big Picture: A Classroom Activity for Organic Chemistry", Thomas Poon makes interesting use of the device exploited by Istvan Banyai in his Zoom books to help students of organic chemistry make connections between the molecular world and ways in which those molecules are important in daily life. The paper should have appeal at all levels of science education from the time the idea of molecules is first introduced through college-level courses. Along the way, students will encounter important biological molecules (such as chlorophyll), inks (such as pen ink), CFCs, hydrocarbon fuels, plastics (such as Lexan polycarbonate), and molecules with medical applications (such as aspirin and novocaine).
Molecular Modeling |
Molecular Properties / Structure
Connected Chemistry  Mike Stieff
Connected Chemistry, a novel learning environment for teaching chemistry, is appropriate for use in both high school and undergraduate chemistry classrooms. Connected Chemistry comprises several molecular simulations designed to enable instructors to teach chemistry using the perspective of emergent phenomena. That is, it allows students to see observed macro-level chemical phenomena, like many other scientific phenomena, as resultant from the interactions of many individual agents on a micro-level. This perspective is especially appropriate to the study of chemistry where the interactions between multitudes of molecules on the atomic level give rise to the macro-level concepts that students study in the classroom. Connected Chemistry comprises molecular simulations embedded in the NetLogo modeling software (1). The collection contains several predesigned simulations of closed chemical systems to teach specific chemistry concepts. Currently, Connected Chemistry contains models for teaching Brønsted Lowry acid base theory, enzyme kinetics, radical polymerization, buffer chemistry, kinetics, chemical equilibrium, and crystallization. Instructors and students can individually tailor the predesigned simulations or generate new simulations as they are needed in the context of a particular lesson, classroom, or department.
Acids / Bases |
Gases |
Kinetics |
Nuclear / Radiochemistry |
pH |
Titration / Volumetric Analysis |
Polymerization |
Equilibrium |
Catalysis
Coumarin, Naphthalene, and Additional Polycyclic Aromatic Hydrocarbons  William F. Coleman
The featured molecules this month are drawn from two papers. The first, "One-Pot Synthesis of 7-Hydroxy-3-carboxycoumarin in Water", is a Green Chemistry feature by Fringuelli, Piermatti, and Pizzo. The three-dimensional versions of the molecules in the synthesis of the coumarin derivative are directly tied to the reaction scheme included in the paper, opening the possibility of showing large numbers of complex synthetic pathways in this manner.The second paper is "Determining the Carbon-Carbon Distance in an Organic Molecule with a Ruler" by Simoni, Tubino, and Ricchi. This article describes an experiment to determine the size of a naphthalene molecule, using an extension of classic experiments for determining molecular size and Avogadro's number. While the structure of naphthalene will come as no surprise to most students, the molecule collection also includes additional polycyclic aromatic hydrocarbons (PAHs) that can be used to introduce students to the environmental and health issues related to these molecules.
Molecular Modeling |
Molecular Properties / Structure |
Aromatic Compounds