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Other Resources: 43 results
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 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 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
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
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 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
Dibenzyl Terephthalate  William F. Coleman, Randall J. Wildman
The WebWare molecule for January is from the article "Chemical Recycling of Pop Bottles: The Synthesis of Dibenzyl Terephthalate from the Plastic Polyethylene Terephthalate" by Craig J. Donahue, Jennifer A. Exline, and Cynthia Warner. Polyethylene terephthalate from 2-liter pop bottles can be recycled by converting it to dibenzyl terephthalate.
Molecular Modeling |
Molecular Properties / Structure
Ascorbic Acid and Methylene Blue  William F. Coleman, Randall J. Wildman
The WebWare molecules of the month for May are featured in several articles in this issue. "Arsenic: Not So Evil After All?" discusses the pharmaceutical uses of methylene blue and its development as the first synthetic drug used against a specific disease. The JCE Classroom Activity "Out of the Blue" and the article "Greening the Blue Bottle" feature methylene blue and ascorbic acid as two key ingredients in the formulation of the blue bottle. You can also see a colorful example of these two molecules in action on the cover. "Sailing on the 'C': A Vitamin Titration with a Twist" describes an experiment to determine the vitamin C (ascorbic acid) content of citrus fruits and challenges students, as eighteenth-century sea captains, to decide the best fruit to take on a long voyage.
Molecular Modeling |
Molecular Properties / Structure
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
Metal Chloride Compounds  William F. Coleman
The WebWare molecules of the month for August stem from the article, "Discovery Videos: A Safe, Tested,Time-Efficient Way To Incorporate Discovery-Laboratory Experiments into the Classroom".
Molecular Modeling |
Molecular Properties / Structure
Crystal Violet, Fluorenone, and Fluorene  William F. Coleman
The WebWare molecules of the month for the month of September are discussed in the article by Gail Horowitz, "A Discovery Approach to Three Organic Laboratory Techniques: Extraction, Recrystallization, and Distillation". In the extraction part of the experiment, students use aqueous washes to remove a highly polar colored contaminent (crystal violet) or a nonpolar colored contaminent (fluorenone) from a desired compound (fluorene).
Molecular Modeling |
Molecular Properties / Structure
Quinine and Urea  William F. Coleman
The WebWare molecules of the month are discussed in two laboratory articles in this issue. Quinine is studied in the article "A Fluorimetric Approach to Studying the Effects of Ionic Strength on Reaction Rates: An Undergraduate Steady-State Fluorescence Laboratory Experiment" by Stephen W. Bigger, Peter J. Watkins, and Bruce Verity. Urea, a typical protein denaturant, is used as a cosolvent in the article "Transfer Free Energy and the Hydrophobic Effect" by Joseph M. Serafin.
Molecular Modeling |
Molecular Properties / Structure
Amylose and Polystyrene  William F. Coleman
The WebWare molecules of the month are amylose and polystyrene, which are examined in JCE Classroom Activity #57: "Pondering Packing Peanuts Polymers". In the activity, students investigate polymers and their chemical composition. The structures below show several repeating units of the two polymers. The helical, 50-unit amylose shows the structure that complexes with iodine to produce the blue charge-transfer complex in the starch iodine test.
Molecular Modeling |
Molecular Properties / Structure
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
Fountain Pen Ink  William F. Coleman
This months Featured Molecules are drawn from the paper Chemical Composition of a Fountain Pen by Inkby J. Martín-Gil, M. C. Ramos-Sánchez, F. J. Martín-Gil, and M. José-Yacamán on the composition and stability of inks.
Molecular Modeling |
Molecular Properties / Structure
Lubricating Greases  William F. Coleman
The Featured Molecules for this month all come from the paper "Lubricating Grease: A Chemical Primer" by Craig Donahue. This paper is a rich source of structural examples ranging from small molecules to metal complexes to polymeric species.
Molecular Modeling |
Molecular Properties / Structure
The Chemistry of Popcorn; Polymers of Glucose  William F. Coleman
The featured molecules this month are all polymers of glucose, and relate to the two papers on the chemistry of popcorn: "Popping Popcorn Kernels: Expanding Relevance with Linear Thinking" by Jordan L. Fantini, Michael M. Fuson, Thomas A. Evans, and "Popcorn What's in the Bag?" by Marissa B. Sherman and Thomas A. Evans.
Molecular Modeling |
Molecular Properties / Structure
Catalysts from the 2005 Nobel Prize in Chemistry  William F. Coleman
The 2005 Nobel Prize for Chemistry celebrated molecules that are of great value to researchers, to the broader society, and to chemical educators. Some of those molecules are featured here.
Molecular Properties / Structure |
Molecular Modeling
The Chemistry of Highly Fluorinated Compounds  William F. Coleman
The featured molecules for January come from the paper Fluorous Compounds and Their Role in Separation Chemistry by Maria Angeles Ubeda and Roman Dembinski. This paper explores the use of highly fluorinated compounds as solvents, catalysts, and reagents.
Molecular Modeling |
Molecular Properties / Structure
Perfume Chemistry; Jasmone, α-Damascone, Geraniol, Civetone, and Musk Baur  William F. Coleman
The featured molecules for the month of January are some of the natural and synthetic molecules used to create perfumes. The chemistry of perfumes is discussed in the article "Chemistry Perfumes Your Daily Life". Jasmone is a natural component of jasmine and a key component for its odor; α-damascone is a natural component of rose oil; geraniol is a synthetic rose odor; civetone is a macrocyclic musk that used to be obtained from the civet cat; and musk baur is a synthetic molecule with a musky smell.
Molecular Modeling |
Molecular Properties / Structure
Polycyclic Aromatic Hydrocarbons  William F. Coleman
The featured molecules for the month of February are a number of polycyclic aromatic hydrocarbons (PAHs) discussed in the article "Fluorescence, Absorption, and Excitation Spectra of Polycyclic Aromatic Hydrocarbons as a Tool for Quantitative Analysis". PAHs are ubiquitous in air, soils, and water as a result of both direct and indirect emissions. PAHs are discharged into environments as byproducts of the combusion of fossil fuels used for transportation and generation of electricity. Other sources of PAH emissions include industrial processes, biomass burning, waste incineration, oil spills, and cigarette smoke.
Molecular Modeling |
Molecular Properties / Structure
Bioorganic Synthesis; Monosodium Glutamate and Other Amino Acids  William F. Coleman
The March featured molecules are discussed in the article "The Monosodium Glutamate Story: The Commercial Production of MSG and Other Amino Acids". This paper provides a number of opportunities for introducing students to the importance of stereochemistry in bioorganic synthesis. The collection here includes all of the relevant molecules in the synthesis of α-amino-ε-aminocaprolactam (ACL). The introduction of two chiral centers in the reaction of cyclohexene with NOCl results in four diastereomers, and it is instructive to ask students to predict the relative abundance of those isomers and the dependence of that distribution on the extent to which the reaction is syn- or anti-addition, and to account for the fact that the resultant oxime, and the ACL, are obtained as racemates.
Molecular Modeling |
Molecular Properties / Structure
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
Boron Clusters  William F. Coleman
The May featured molecules are discussed in the Viewpoints article "Boron Clusters Come of Age". The review paper by Russell N. Grimes on boron clusters reminds us both of the past impact that these interesting structures have had on the development of our understanding of cluster chemistry and on the future development of what one might refer to as "post-fullerene" clusters. The wide range of structures found in this paper admirably illustrate the structural flexibility arising from clusters of a variety of symmetries and degrees of boron replacement with carbon and other atoms.
Molecular Modeling |
Molecular Properties / Structure
Enantiomer Specificity in Pharmaceuticals  William F. Coleman
The molecules of the month this month come from three papers: Demonstration of Enantiomer Specificity of Proteins and Drugs by Gretchen L. Anderson, Incorporation of Medicinal Chemistry into the Organic Chemistry Curriculum by David C. Forbes, and Infusing the Chemistry Curriculum with Green Chemistry Using Real-World Examples, Web Modules, and Atom Economy in Organic Chemistry Courses by Michael C. Cann and Trudy A. Dickneider.The authors of these papers use molecules whose names at least are familiar to the majority of students to introduce important structural and synthetic concepts. A particularly poignant example is that of thalidomide, in which the two enantiomers produce dramatically, and in the case of the S form tragically, different results. In addition to demonstrating enantiospecific reactivity, the thalidomide case is a good starting point for a discussion of how chemists ask questions, what questions we should be asking, and whether or not it is possible to minimize, if not completely eliminate, unintended consequences.
Molecular Modeling |
Molecular Properties / Structure
Chocolate; Theobromine and Caffeine  William F. Coleman
The featured molecules this month come from "Chocolate: A Marvelous Natural Product of Chemistry" by Ginger Tannenbaum. As discussed in the article, chocolate is a natural food and is a mixture of many chemical compounds; approximately 400 compounds have been identified in chocolate following fermentation and processing. During processing, a liquid called "chocolate liquor" is formed that is composed of about 55% fat, 17% carbohydrate, 11% protein, and most of the remainder is tannins and ash. Depending on its source, it may also contain theobromine, an alkaloid related to caffeine, in quantities ranging from 0.8% to 1.7%. Caffeine is found in lesser quantities. Theobromine and caffeine are both methyl-xanthines. Theobromine is a smooth muscle stimulant, while caffeine is predominately a central nervous system stimulant. When solidified, the liquor forms bitter (unsweetened) cooking or baking chocolate.
Molecular Modeling |
Molecular Properties / Structure
Alkaloids; Strychnine, Codeine, Heroin, and Morphine  William F. Coleman
The featured molecules this month come from the article "The Conversion of Carboxylic Acids to Ketones: A Repeated Discovery" by John W. Nicholson and Alan D. Wilson. The authors describe the repeated discovery of this reaction and illustrate its central role in Woodward's total synthesis of strychnine. Strychnine is a member of a large class of nitrogen heterocycles known as alkaloids, a name derived from the fact that all produce basic solutions in water. Other well-known members of this class of compounds, all of which are pharmacologically active, are nicotine, atropine (deadly nightshade), quinine, lysergic acid, cocaine, and the three structurally similar compounds codeine, heroin, and morphine.
Molecular Modeling |
Molecular Properties / Structure
Chemistry of Blood Type  William F. Coleman
The molecules for this month come from the paper Glycosyltransferases A and B: Four Critical Amino Acids Determine Blood Type by Rose, Palcic, and Evans on structural factors determining blood type. Included are interactive molecule files for the three determinant molecules and the two donors.
Molecular Modeling |
Molecular Properties / Structure
Azulene Chemistry  William F. Coleman
The month's featured molecules come from the paper An Azulene-Based Discovery Experiment: Challenging Students To Watch for the "False Assumption" by Charles Garner illustrating some of the chemistry of a substituted azulene. Azulene is a structural isomer of naphthalene and differs from it in several important ways, the most obvious being azulene's intense blue color, which arises from the S0 → S2 transition. Another unusual feature of this molecule is that its fluorescence arises from the reverse of this transition rather than from S1 → S0.
Molecular Modeling |
Molecular Properties / Structure
Menthol Steioisomers  William F. Coleman
The JCE Featured Molecules for July come from the paper An Engaging Illustration of the Physical Differences among Menthol Stereoisomers by Edward M. Treadwell and T. Howard Black on the use of commercially available stereoisomers of menthol to illustrate properties of enantiomers and diastereomers. The paper describes the use of four of the eight possible stereoisomers. Structures of all eight stereoisomers are included in this month's molecule collection, labeled by the chirality of the three chiral atoms. In addition to the exercises described in the paper, students can be asked to match the appropriate structures to those shown in the paper, or to generate structures for the isomers that are not discussed.
Molecular Modeling |
Molecular Properties / Structure
Weekly Molecules; A Cure for the 830 a.m. Blues  William F. Coleman
The concept of an online molecule of the time period, day, week, or month, as in the case of this column has increased in popularity since the initial Web sites created at a number of British universities in the mid-1990s. The paper, 8:31 a.m. Belly Flop: Attitude Adjustment through Weekly Feature Molecules by Sonya Franklin, Norbert Pienta, and Melissa Fry describes a study of student responses to a molecule of the week program. Some of the results from their surveys of students indicate that the program indeed helps students place the chemistry that they are learning into a broader societal context. Visualizing these molecules in three dimensions helps students who have difficulty going from the two-dimensional drawing to the details of structure and stereo-chemistry. Some of the recent controversy that followed the now infamous comments by Harvard President Lawrence Summers, brought up, once again, the debate over whether men and women have different abilities to visualize in three dimensions. Many of us have seen a lot of evidence that such a difference is not necessarily gender based, but we should be focusing attention on ensuring that such differences are not determining factors for students' success in science. At one time students who could not titrate well were discouraged from becoming chemists. We should make certain that we are not discouraging students for equally unimportant reasons.
Molecular Modeling |
Molecular Properties / Structure
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
Parallel Combinatorial Synthesis of Azo Dyes  William F. Coleman
The featured molecules for this month are from "Parallel Combinatorial Synthesis of Azo Dyes: A Combinatorial Experiment Suitable for Undergraduate Laboratories" by Benjamin W. Gung and Richard T. Taylor. The principle of combinatorial chemistry is illustrated by generating a relatively large number of colorful dyes using only one common reaction, the diazo coupling, and two common reactants with small variations. Fully manipulable (Chime) versions of these molecules appear below.
Molecular Modeling |
Molecular Properties / Structure
Mol4D: A Web-Based Computational Chemistry Interface for Educational Purposes  Oliver Stueker, Ingo Brunberg, Gregor Fels, Hens Borkent, Jack van Rooij
Mol4D (Molecules in Four Dimensions) is a web and Chime based molecule editor and computational interface. Visualization and interactivity are the predominant features. Computational results, based on MOPAC, are obtained within seconds and structures presented using the Chime plug in. Orbital information (in VRML format) and the selection of parameters for a linear or grid scan are options.
Computational Chemistry |
Molecular Modeling |
Molecular Mechanics / Dynamics
Photochemical Oxidation of Bilirubin to Biliverdin  William F. Coleman
The Featured Molecules from September come from the article Solar Irradiation of Bilirubin: An Experiment in Photochemical Oxidation by F. M. Salih and A. E. Pillay.
Molecular Modeling |
Molecular Properties / Structure |
Photochemistry
Copper and Nickel Complex Ions  William F. Coleman
The Featured Molecules this month come from Donald C. Bowmans article A Colorful Look at the Chelate Effect, the final Overhead Projector Demonstrations column edited by the late Doris Kolb. Included in the online collection are all eight isomeric forms of [Ni(en)3]2+, demonstrating the effects of ligand backbone conformation.
Molecular Modeling |
Amino Acids |
Molecular Properties / Structure
Amino Acids  William F. Coleman
The Featured Molecules this month are the 20 standard α-amino acids found in proteins and serve as background to the paper by Barone and Schmidt on the Nonfood Applications of Proteinaceous Renewable Materials. The molecules are presented in two formats, the neutral form and the ionized form found in solution at physiologic pH.
Molecular Modeling |
Amino Acids |
Molecular Properties / Structure
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
Microwave-Assisted Heterocyclic Chemistry  William F. Coleman
The featured molecules for this month come from the Green Chemistry article, "Microwave-Assisted Heterocyclic Chemistry for the Undergraduate Organic Laboratory" by Musiol, Tyman-Szram, and Polanski.
Molecular Modeling |
Molecular Properties / Structure |
Heterocycles
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
Web-Based Interactive Animation of Organic Reactions  Ingo Brunberg, Gregor Fels, Hens Borkent, Jack van Rooij, Oliver Stueke
This WWW-based service for the automated animation of organic reactions we believe to be a versatile tool for teaching and learning organic chemistry. It allows the investigation of the influence of substituents of starting materials on the reaction coordinate and the energy of the depicted reaction. Starting from a list of precalculated organic reactions hydrogen atoms can be substituted by a variety of organic substituents and functional groups using the molecule editor. The new set of starting material is submitted to the calculation of intrinsic reaction coordinates that yields automatically an animation of the reaction that can be viewed with the Chime plugin.
Computational Chemistry |
Molecular Modeling |
Molecular Mechanics / Dynamics |
Enrichment / Review Materials
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