71 Results
A Pedagogical Simulation of Maxwell's Demon Paradox   
(Software, Instructional Material (1))
Maxwell's demon was conceived by James Clerk Maxwell in 1871 to illustrate the statistical basis of thermodynamics (1), and the concept has since formed an arena for investigation and clarification of many concepts in thermodynamics (2). Chemistry students often have difficulty developing an intuitive knowledge of some concepts in thermodynamics. A Pedagogical Simulation of Maxwell's Demon aims to help make these concepts more understandable for students. Teaching thermodynamics from the microscopic point of view can help students develop an intuitive understanding of its concepts. This program simulates, at the microscopic level, two gas chambers with an opening between them. The program allows students or their instructors to set up simulations that illustrate the thermodynamics and statistical behavior of the system. The user determines the basis for whether the demon permits or denies passage of particles through the opening using information from the microscopic level, such as specific particle velocity. Students can track and analyze how this affects particle distribution, thermal equilibrium, relaxation time, diffusion, and distribution of particle velocities.
A Method of Visual Interactive Regression   
(Software, Instructional Material (1))
Over the past decade many colleges and universities have placed increased emphasis on having students develop statistical and data analysis skills in a range of disciplines. Some institutions now require that all students complete at least one course with a strong component of data analysis, whether the data are from chemical experiments, the census, or some other source. As chemists, one of our concerns should be to ensure that students view data analysis as an integral part of any quantitative experiment, and, as far as possible, do not treat this process as a black box. The authors of A Method of Visual Interactive Regression, a spreadsheet application, have developed a visual approach to linear least-squares curve fitting that drives home the idea of minimizing the sum of the squares of the deviations in order to find the best fit to a set of data that are being described by a linear relationship. For many students these visualizations are likely to persist a great deal longer than the mathematical derivations of the equation for the slope and the intercept. The visualizations will provide a useful connection between a set of equations and the buttons on a calculator or the insertion of a trendline in a spreadsheet.
Visualizing Numerical Methods (2)   
(Software, Instructional Material (1))
These movies are designed to help students visualize various numerical approaches to evaluating functions or solving equations. The methods themselves may be familiar to students from their mathematics courses, but they may have forgotten the material or never made the connection between a statement such as "the derivative of a curve at a given point is the slope of the line tangent to the curve at that point" and the way that one might evaluate such a derivative. All of the movies have VCR-style controls that enable the student to step through them one frame at a time and to move backwards as well as forwards.
Principles of Gel Permeation Chromatography   
(Software, Instructional Material (1))
Principles of Gel Permeation Chromatography presents the principles of gel permeation chromatography (GPC) for students in introductory undergraduate courses of chemistry and biochemistry. These principles are presented in four sections: Introduction, Real Lab, Virtual Lab, and Microscopic Model. The Introduction and Real Lab sections present a brief view of the basic experimental apparatus typically used in laboratory GPC in order to provide a concrete connection of the real process of separation. The basic elements of column chromatography, emphasizing the stationary and mobile phases, are presented in the Introduction, followed by a sequence of pictures and texts describing major steps in GPC analysis in the Real Lab section. The Virtual Lab section is a simulator. Three samples are available for a virtual GPC experiment: sample 1, containing hemoglobin; sample 2, containing methylene blue; and sample 3, containing both methylene blue and hemoglobin. Each sample undergoes a virtual separation run, which is dynamically represented in three ways in the software: a virtual column, the collected fractions, and a virtual chromatogram. This threefold representation allows the simultaneous view of key aspects of the process to demonstrate the correlation between the experimental procedure and the resulting chromatogram.
Universal Algorithm for Acid-Base Equilibrium Calculations   
(Software, Instructional Material (1))
These Microsoft Excel workbooks facilitate the calculation of the equilibrium composition of simple to complex acid-base systems. Three workbooks are available: 1. pH-mix calculates the equilibrium composition for any mixture of protolytes. 2. pH-titr calculates and presents titration curves. 3. pH-titrd calculates and presents titration curves with derivative curves included. The workbooks require only basic knowledge about Excel and almost no calculation abilities. However, they do require a description of chemical properties of the system components. Thus they allow students to concentrate on chemistry skills rather than laborious algebra and arithmetic.
Periodic Table Live! Tutorial (part II)   
(Other (1))
Look here for a tutorial to guide you through the use of the Periodic Table Live! It is in the form of 2 power point files which you can download. We recommend opening up your web browser and trying things out as the power point suggests.
Molecular Models of Indicators   
(Interactive Simulation (1))
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 Models of Annatto Seed Components   
(Interactive Simulation (1))
In January 2008 the focus of this column was on the plant pigments lycopene and beta-carotene (1). Our attention this month returns to two papers discussing the pigments in annatto seeds (Figure 1), including direct precursors to lycopene. The paper by Teixeira, Dur�n, and Guterres describes the extraction and encapsulation of annatto seed components (2). The McCullagh and Ramos paper describes the separation of the pigment bixin from these seeds by TLC and column chromatography (3). These molecules could form the basis of interesting exercises across the chemistry curriculum. In courses designed for non-majors, students could choose a molecule from the table and search the literature for both scientific and non-scientific sources. Are the claims made in the latter sources regarding the health benefits of these molecules consistent with the scientific data? That discussion could be expanded to the more general question of how one tests the validity of statements made in what are essentially advertisements. Are any of these precursor molecules to lycopene considered to have anticancer properties (4)? In introductory or general chemistry courses, students could explore the various bond lengths and bond angles in the molecules to see whether they are consistent with their expectations based on simple bonding models. In introductory, organic, or biochemistry classes, the thermodynamics of hydrogenation and dehydrogenation could be examined. This might make an interesting alternative to the oft-discussed Haber Process. What conditions would one propose for a dehydrogenation process? Why are dehydrogenation reactions important? What enzymes catalyze the various dehydrogenation steps from phytoene to lycopene? These molecules could also be used in a variety of computational exercises in introductory and physical chemistry courses. Hartree�Fock calculations on a molecule such as phytoene may prove time-consuming depending on the nature of the computing system available. A good place to begin would be to perform semi-empirical calculations on the various molecules. Do the optimized structures match experimental results or the results of larger calculations? Does the HOMO�LUMO gap correlate with the observed electronic absorption spectra? Which is more important in determining the difference in absorption between phytoene and phytofluene, the total number of double bonds or the number of bonds in the region of conjugation? Of course the aspect of these molecules that is most likely to capture student attention is their color, and they provide nice examples of the origin of color, the relationship between color observed and color absorbed, and, in upper level courses, the more detailed relationships of the energies of the ground and excited states.
Molecular Models of Leaf Extracts   
(Interactive Simulation (1))
Our Featured Molecules this month come from the paper by Pelter et. al. on the analysis of leaf extracts by thin-layer chromatography (1). As the authors discuss, their experiment may be used in courses at various levels of the curriculum. The molecules discussed in the paper are also of wide interest both for their structural properties and their wide-ranging appearance in both natural and synthetic substances. Included in the molecule collection are all of the isomers for the molecules pictured in the text with the exception of menthyl acetate, for which only one structure is given (see below). All of these molecules have been optimized at the HF/631-G(d) level. The menthol family enantiomeric pairs of menthol, isomenthol, neomenthol and neoisomenthol provide a rich yet coherent group of molecules on which to base discussion of chirality, enantiomers and diastereomers. Treadwell and Black have described some of the differences in physical properties of four members of this family, and several other experiments using one or more menthols have been published in this Journal (2, 3). I have created a Web page in which the eight molecules are embedded in no particular order, and with no rational file names. This is being used in at least one of our organic sections to give students experience at identifying enantiomers, and diastereomers, and in applying R/S notation (4). As access to computational software becomes more common, and as efforts are being made to incorporate more relevant modeling experiments into all levels of the curriculum, the menthols again present some interesting possibilities. While students at the organic level know about enantiomers differing in their optical rotation, and about chiral molecules interacting with chiral and achiral environments, it is instructive for them to think of other ways in which enantiomers and diastereomers are the same or different. Three useful ways of checking to see whether two structures are truly enantiomers is to compute their total energies, vibrational spectra, and dipole moments. These calculations are available in most common computational packages. Figure 1 shows the results of energy calculations on optimized structures of the eight isomers. The enantiomeric pairs have, as expected, exactly the same total energy, while the various diastereomers differ in energy. The computation of the vibrational spectra is a very sensitive probe to determine whether two structures are optimized and enantiomeric or not. Structures that are almost enantiomeric, but not quite optimized, may exhibit similar energies, but the low frequency vibrations will be sensitive to any deviation from optimization. If two supposedly enantiomeric structures do not have the same computed vibrations, or if either shows a negative frequency, the structures need to be optimized more carefully. As with the vibrational frequencies, enantiomers should show identical dipole moments. Only one structure of the eight isomers in the menthyl acetate family is included in the collection, giving students the chance to build the other seven and verify their computed properties. Because of the central role that chirality plays in chemistry, and particularly in biochemistry, it seems appropriate to introduce some of these visualization and modeling exercises early in the curriculum, and in courses designed for students majoring in other areas. Students in various courses could pursue other aspects of these same molecules including odor and cooling properties, and green chemistry approaches to synthesizing menthols.
Molecular Models of Lycopene and Other Carotenoids   
(Interactive Simulation (1))
Over the past decade or so the phrase emerging research suggests has entered the argot of advertising, and that phrase has been applied to this month's Featured Molecule, lycopene, particularly with regard to potential health benefits of tomatoes. The paper by Jie Zhu, Mingjie Zhang, and Qingwei Liu (1) describes an extraction and purification of lycopene from tomato paste using an emulsion rather than the traditional solvent-based extraction. Lycopene is a member of the family of molecules called carotenoids, the most familiar of which is beta-carotene. This family of natural products includes more than 500 members that have been isolated and whose structures have been determined. Professor Hanspeter Pfander's research group at the University of Bern maintains a Web site with a significant amount of information on carotenoid structure, synthesis, and activity (2). Structurally one can think of carotenoids as consisting of three segments, a relatively rigid conjugated central portion with end groups. The end groups are, in general, flexible with respect to rotation about the bond connecting them to the central portion. For example, in beta-carotene, the dependence of total energy on the dihedral angle shown in Figure 1, displays a very broad range of essentially isoenergetic conformations (Figure 2). The energies shown in Figure 2 were calculated at the PM3 level using Hyperchem 7.5 (3). Calculations at the HF/631-G(d,p) level, with many fewer data points, show a similar trend. Many of the health benefits derived from various carotenoids are attributed to their antioxidant activities. Carotenoids react with singlet-oxygen in a physical, diffusion-controlled, quenching process that results in ground state triplet-oxygen and, following a non-radiative relaxation, ground state carotenoid. Of the various carotenoids that have been studied, lycopene and beta-carotene show the greatest quenching rate constants (4). The carotenoids provide us with countless explorations by students and teachers looking for connections between fundamental chemical concepts and real-world applications. Structure, reactivity, chemical synthesis, biosynthesis, and stereochemistry are just a few of the concepts involved in understanding the manifest important roles that these molecules play.
Molecular Models of Antioxidants and Radicals   
(Interactive Simulation (1))
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.
Molecular Models of Products and Reactants from Suzuki and Heck Syntheses   
(Interactive Simulation (1))
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.
Molecular Models of Reactants and Products from an Asymmetric Synthesis of a Chiral Carboxylic Acid   
(Interactive Simulation (1))
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.
Molecular Models of Real and Mock Illicit Drugs from a Forensic Chemistry Activity   
(Interactive Simulation (1))
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?
Collection of Chiral Drug, Pesticide, and Fragrance Molecular Models   
(Interactive Simulation (1))
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.
Molecular Models of Dyes   
(Interactive Simulation (1))
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).
Molecular Models of Rosmarinic Acid and DPPH   
(Interactive Simulation (1))
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).
Molecular Models of DAPI   
(Interactive Simulation (1))
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.
Molecular Models of DNA   
(Interactive Simulation (1))
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.
Molecular Models of Peroxides and Albendazoles   
(Interactive Simulation (1))
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?
Photosystem II Oxygen-Evolving Complex   
(Interactive Simulation (1))
Both introductory texts and texts for upper-level inorganic chemistry courses are shifting the emphasis in their coverage of transition metal chemistry from classical Werner complexes to those that exhibit some form of catalytic activity. This is of particular importance to bioinorganic chemistry, a now mature area of the science, but one that is still underrepresented in the undergraduate curriculum. Derrick L. Howard, Arthur D. Tinoco, Gary W. Brudvig, John S. Vrettos, and Bertha Connie Allen address this issue in their paper Catalytic Oxygen Evolution by a Bioinorganic Model of the Photosystem II Oxygen-Evolving Complex by a dimanganese complex that is proposed as a model for the four-manganese center in Photosystem II. The featured molecules for May are the model compound in the proposed mechanism for oxygen production.
Electrostatics Attraction (GCMP)   
(Interactive Simulation, Software (1))
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.
Water #2 (GCMP)   
(Interactive Simulation, Software (1))
Water #2: this is a resource in the collection "General Chemistry Multimedia Problems". Isotopes are forms of the same element composed of atoms that have different numbers of neutrons. In this problem we will begin by observing the properties of water containing two isotopes of hydrogen. 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.
Water #1 (GCMP)   
(Interactive Simulation, Software (1))
Water #1: this is a resource in the collection "General Chemistry Multimedia Problems". Isotopes are forms of the same element composed of atoms that have different numbers of neutrons. In this problem we will begin by observing the properties of water containing two isotopes of hydrogen. 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.
Two Solids (GCMP)   
(Interactive Simulation, Software (1))
Two Solids: this is a resource in the collection "General Chemistry Multimedia Problems". When two solids barium hydroxide octahydrate, Ba(OH)2. 8H2O and ammonium thiocyanate, NH4SCN are mixed, they react. We will explore the thermodynamics of the reaction. 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.
Two Balloons (GCMP)   
(Interactive Simulation, Software (1))
Two Balloons: this is a resource in the collection "General Chemistry Multimedia Problems". In the Two Balloons video, the left flask contains some water and the right flask contains only air. What do you see when balloons are fastened to the mouths of the hot flasks? 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.
Strong Acids (GCMP)   
(Interactive Simulation, Software (1))
Strong Acids: this is a resource in the collection "General Chemistry Multimedia Problems". This problem will explore the properties of common strong acids. 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.
Steam (GCMP)   
(Interactive Simulation, Software (1))
Steam: this is a resource in the collection "General Chemistry Multimedia Problems". We observe two videos of steam produced by boiling water. The steam is channeled through a copper coil which will be heated. 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.
Phlogiston (GCMP)   
(Interactive Simulation, Software (1))
Phlogiston: this is a resource in the collection "General Chemistry Multimedia Problems". In this problem we will think back to the last half of the 18th century when modern chemistry was beginning to take place. One of the major problems occupying chemists at the time was combustion. The dominant theory of combustion in the mid-18th century involved a substance called "phlogiston." 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.
Paramagnetism (GCMP)   
(Interactive Simulation, Software (1))
Paramagnetism: this is a resource in the collection "General Chemistry Multimedia Problems". In this problem we will begin by observing the magnetism of three manganese compounds. These compounds have been placed in capsules, which will be pulled toward a magnet if the compound is paramagnetic. 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.
Oxides (GCMP)   
(Interactive Simulation, Software (1))
Oxides: this is a resource in the collection "General Chemistry Multimedia Problems". In this problem we will explore the properties of the oxides of a few elements. We will add samples of the oxides to universal indicator solution and learn about the acid-base character of the oxides. 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.
NO and O2 #3 (GCMP)   
(Interactive Simulation, Software (1))
NO and O2 #3: this is a resource in the collection "General Chemistry Multimedia Problems". NO and O2 and the product of the corresponding reaction are three gases which have different solubilities in water. 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.
NO and O2 #2 (GCMP)   
(Interactive Simulation, Software (1))
NO and O2 #2: this is a resource in the collection "General Chemistry Multimedia Problems". NO and O2 and the product of the corresponding reaction are three gases which have different solubilities in water. 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.
NO and O2 (GCMP)   
(Interactive Simulation, Software (1))
NO and O2: this is a resource in the collection "General Chemistry Multimedia Problems". NO and O2 and the product of the corresponding reaction are three gases which have different solubilities in water. 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.
Nitrogen Oxides (GCMP)   
(Interactive Simulation, Software (1))
Nitrogen Oxides: this is a resource in the collection "General Chemistry Multimedia Problems". Two of the most important nitrogen oxides, N2O4 and NO2, are in equilibrium with each other. We are interested in how this equilibrium shifts with temperature. 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.
Metals 2 (GCMP)   
(Interactive Simulation, Software (1))
Reactions of Metals 2: this is a resource in the collection "General Chemistry Multimedia Problems". In this problem we will observe the reactions of different metals (Zn, Ni, Mn, Fe) with iodine. 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.
Metals 1 (GCMP)   
(Interactive Simulation, Software (1))
Reactions of Metals 1: this is a resource in the collection "General Chemistry Multimedia Problems". In this problem we will observe the reactions of different metals (Zn, Ni, Mn, Fe) with iodine. 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.
Hexane 2 (GCMP)   
(Interactive Simulation, Software (1))
Hexane 2: this is a resource in the collection "General Chemistry Multimedia Problems". Hexane, a liquid hydrocarbon with the formula C6H14, burns when ignited in the presence of oxygen. In this problem we will observe videos of this combustion reaction. 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.
Hexane 1 (GCMP)   
(Interactive Simulation, Software (1))
Hexane 1: this is a resource in the collection "General Chemistry Multimedia Problems". Hexane, a liquid hydrocarbon with the formula C6H14, burns when ignited in the presence of oxygen. In this problem we will observe videos of this combustion reaction. 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.
Halogens and Halides (GCMP)   
(Interactive Simulation, Software (1))
Halogens and Halides: this is a resource in the collection "General Chemistry Multimedia Problems". In this problem we will study the oxidation-reduction reactions between the halogens and the halide ions. The halogens and halides will be dissolved in water and hexane. 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.
Floating Squares (GCMP)   
(Interactive Simulation, Software (1))
Floating Squares: this is a resource in the collection "General Chemistry Multimedia Problems". In this problem we will coat a piece of notecard with graphite (from pencil lead). We then will float the piece in two beakers containing water and a second solvent. 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.
Fireworks (GCMP)   
(Interactive Simulation, Software (1))
Fireworks: this is a resource in the collection "General Chemistry Multimedia Problems". In this problem we will study the colors produced by metal salts in flames. 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.
Electrolisis 3 (GCMP)   
(Interactive Simulation, Software (1))
Electrolisis of Water #3: this is a resource in the collection "General Chemistry Multimedia Problems". In this problem we will contrast the electrolysis of water with boiling. 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.
Electrolisis 2 (GCMP)   
(Interactive Simulation, Software (1))
Electrolisis of Water #2: this is a resource in the collection "General Chemistry Multimedia Problems". In this problem we will contrast the electrolysis of water with boiling. 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.
Electrolisis 1 (GCMP)   
(Interactive Simulation, Software (1))
Electrolisis of Water #1: this is a resource in the collection "General Chemistry Multimedia Problems". In this problem we will contrast the electrolysis of water with boiling. 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.
Drinking Bird (GCMP)   
(Interactive Simulation, Software (1))
Drinking Bird: this is a resource in the collection "General Chemistry Multimedia Problems". The drinking bird's felt-covered head dips into the beaker of water as it bobs up and down. The tube goes from the bottom of the body to its head. 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.
Disorder (GCMP)   
(Interactive Simulation, Software (1))
Disorder: this is a resource in the collection "General Chemistry Multimedia Problems". A spontaneous change is one that has a natural tendency to occur without needing to be driven by an external influence. This problem will explore the influence of entropy, a measure of disorder, on the spontaneity of a few processes. 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.
Chromate-Dichromate (GCMP)   
(Interactive Simulation, Software (1))
Chromate/Dichromate: this is a resource in the collection "General Chemistry Multimedia Problems". In this problem we will study shifts in the equilibrium between chromate and dichromate. 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.
Burning Magnesium (GCMP)   
(Interactive Simulation, Software (1))
Burning Magnesium: this is a resource in the collection "General Chemistry Multimedia Problems". In this problem we will look at the reactions of two elements with oxygen in air. We will begin by observing the reaction of magnesium metal with oxygen when the metal is heated in air. 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.
Cannon (GCMP)   
(Interactive Simulation, Software (1))
H2 and Cl2 cannon: this is a resource in the collection "General Chemistry Multimedia Problems". In this problem we observe the reaction of hydrogen and chlorine and explore some related reactions. The reaction involves a radical mechanism initiated by light. 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.
Ammonia (GCMP)   
(Interactive Simulation, Software (1))
Ammonia fountain: this is a resource in the collection "General Chemistry Multimedia Problems". In an ammonia fountain, a flask is filled with ammonia gas. A tube from the flask extends into a pan of water that contains phenolphthalein. When a rubber bulb full of water is squeezed, the water squirts into the flask. Water from the pan then is pushed into the flask and the indicator changes color. 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.
Acids and Salts (GCMP)   
(Interactive Simulation, Software (1))
Acids and Salts: this is a resource in the collection "General Chemistry Multimedia Problems". This problem will explore a few properties of common acids and their salts. 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.
Acids (GCMP)   
(Interactive Simulation, Software (1))
Acids: this is a resource in the collection "General Chemistry Multimedia Problems". We will observe the reaction of sodium bicarbonate with three acid solutions. 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.
Solid State Resources, 2nd Edition   
(Interactive Simulation, Software (1))
Solid State Resources helps instructors integrate materials science examples into introductory chemistry courses. It includes the complete Teaching General Chemistry: A Materials Science Companion in pdf, movies, slide shows, overhead masters and the Solid State Model Kit.
Quantum States of Atoms and Molecules   
(Interactive Simulation, Software (1))
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.
A Window on the Solid State   
(Instructional Strategy, Interactive Simulation (1))
A Window on the Solid State helps students understand and instructors present the structural features of solids. Parts I and II were published previously by JCE Software (1) and Macintosh versions of Parts I and II are also available (2). Parts I and II have been updated to include improvements in art and minor changes in logic. Parts III and IV expand the collection to include the structures of simple ionic solids using the visual effects available in an interactive computer medium. The package provides a tour of the structures commonly used to introduce features of the solid state.
Atomic Radius Worksheet   
(Instructional Material (1))
In this course you can find worksheets to use in your classes or to assign as homework assignments that teach various concepts about the periodic table using the free ChemEd DL resource, the Periodic Table Live!(PTL!).
Periodic Table Live! Tutorial (part I)   
(Instructional Material (1))
Look here for a tutorial to guide you through the use of the Periodic Table Live! It is in the form of 2 power point files which you can download. We recommend opening up your web browser and trying things out as the power point suggests.
Questions the Periodic Table Live! can help answer   
(Instructional Material (1))
List of questions PTL can help students answer.
General Exploration Worksheet   
(Instructional Material (1))
In this course you can find worksheets to use in your classes or to assign as homework assignments that teach various concepts about the periodic table using the free ChemEd DL resource, the Periodic Table Live!(PTL!).
Ionization Energy Worksheet   
(Instructional Material (1))
In this course you can find worksheets to use in your classes or to assign as homework assignments that teach various concepts about the periodic table using the free ChemEd DL resource, the Periodic Table Live!(PTL!).
Electron Affinity Worksheet   
(Instructional Material (1))
In this course you can find worksheets to use in your classes or to assign as homework assignments that teach various concepts about the periodic table using the free ChemEd DL resource, the Periodic Table Live!(PTL!).
Carbon Worksheet   
(Instructional Material (1))
In this course you can find worksheets to use in your classes or to assign as homework assignments that teach various concepts about the periodic table using the free ChemEd DL resource, the Periodic Table Live!(PTL!).
Electronegativity Worksheet   
(Instructional Material (1))
In this course you can find worksheets to use in your classes or to assign as homework assignments that teach various concepts about the periodic table using the free ChemEd DL resource, the Periodic Table Live!(PTL!).
Stereochemistry Tutorial   
(Instructional Material (1))
Master the concepts organic stereochemistry with this interactive tutorial. It includes definitions, different three dimensional representations, assigning priorities to stereocenters, and determining the stereochemical relationship between molecules. Each section is followed by a question set that tests knowledge and understanding.
Molecular Models of Volatile Organic Compounds   
(Article (1))
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 Models of Components in Red Bull Energy Drinks   
(Article (1))
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 Models of Compounds in Lightsticks   
(Article (1))
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 Models of Natural Products   
(Article (1))
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.)
Molecular Models of Polymers Used in Sports Equipment   
(Article (1))
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).
Molecular Models of EDTA and Other Chelating Agents   
(Article (1))
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.