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4 Journal Articles
43 Other Resources
Journal Articles: First 3 results.
Molecular Visualization in Science Education: An Evaluation of the NSF-Sponsored Workshop  Thomas J. José and Vickie M. Williamson
This report discusses the perceptions and recommendations of participants who attended an invitational workshop on molecular visualization. The Workshop on Molecular Visualization in Science Education sought to encourage collaboration among diverse communities and promote interdisciplinary research in molecular visualization. A group of research scientists, cognitive scientists, chemical and science educators, and software developers participated. As part of the evaluation of this NSF-funded project, changes in attitude and behavior were measured through observation, pre- and post-workshop surveys given onsite, and a one-year follow-up questionnaire.
José, Thomas J.; Williamson, Vickie M. J. Chem. Educ. 2005, 82, 937.
Conferences |
Enrichment / Review Materials |
Molecular Mechanics / Dynamics |
Molecular Modeling |
Professional Development
Teaching Chemistry with Electron Density Models  Gwendolyn P. Shusterman and Alan J. Shusterman
This article describes a powerful new method for teaching students about electronic structure and its relevance to chemical phenomena. This method, developed and used for several years in general chemistry and organic chemistry courses, relies on computer-generated three-dimensional models of electron density distributions.
Shusterman, Gwendolyn P.; Shusterman, Alan J. J. Chem. Educ. 1997, 74, 771.
Learning Theories |
Computational Chemistry |
Molecular Modeling |
Quantum Chemistry |
Atomic Properties / Structure |
Covalent Bonding |
Ionic Bonding |
Noncovalent Interactions
Chemical education and spatial ability  Barke, Hans-Dieter
Before presenting many of the models students see in 2-D, it is helpful for a chemistry instructor to understand the cognitive science behind spatial ability.
Barke, Hans-Dieter J. Chem. Educ. 1993, 70, 968.
Learning Theories |
Women in Chemistry |
Molecular Modeling
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Other Resources: First 3 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
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