Integrating Computational Molecular Modeling into the Undergraduate Organic Chemistry Curriculum

2009 ◽  
Vol 86 (8) ◽  
pp. 955 ◽  
Author(s):  
Allen D. Clauss ◽  
Stephen F. Nelsen
Keyword(s):  
Organic Chemistry ◽  
Molecular Modeling ◽  
Chemistry Curriculum ◽  
Computational Molecular Modeling

Introduction: Why oxygen chemstry?

1992 ◽  
Author(s):  
Donald T. Sawyer ◽  
R. J. P. Williams
Keyword(s):  
Organic Chemistry ◽  
Nineteenth Century ◽  
Chemical Properties ◽  
First Year ◽  
Chemistry Curriculum ◽  
Design And Synthesis ◽  
Carbon Molecules ◽  
Living Organisms ◽  
Fixed Array ◽  
Oxygen Atoms

The fundamental premise of chemistry is that all matter consists of molecules. The physical and chemical properties of matter are those of the constituent molecules, and the transformation of matter into different materials (compounds) is the result of their reactions to form new molecules. A molecule consists of two or more atoms held in a relatively fixed array via valence-electron orbital overlap (covalent bonds; chemical bonds). In the nineteenth century chemists focused on the remarkable diversity of molecules produced by living organisms, which have in common the presence of tetravalent carbon atoms. As a result the unique versatility of carbon for the design and synthesis of new molecules was discovered, and the subdiscipline of organic chemistry (the science of carbon-containing molecules) has become the dominant part of the discipline. Clearly, the results from a focus on carbon-based chemistry have been immensely useful to science and to society. Although most molecules in biological systems [and produced by living organisms (particularly aerobic systems)] contain oxygen atoms as well as carbon and hydrogen (e.g., proteins, nucleic acids, carbohydrates, lipids, hormones, and vitamins), there has been a long tradition in all of chemistry to treat oxygen atoms as “neutral counterweights” for the “important,” character-determining elements (C, H, Al, Si, Fe, I) of the molecule. Thus, chemists have tended to take the most important element (oxygen) for granted. The chemistry curriculum devotes one or two year-courses to the chemistry of carbon (“Organic Chemistry”), but only a brief chapter on oxygen is included in the first-year and the inorganic courses. However, if the multitude of hydrocarbon molecules is from the incorporation of oxygen atoms in single-carbon molecules argues against the assignment of a “neutral character” for oxygen atoms [e.g., Cn(graphite), CH4(g), CH3OH(1), CH2(O)(1), HC(O)OH(1), (HO)2C(O)(aq), CO(g), CO2(g)]. Just as the focus of nineteenth century chemists on carbon-containing molecules has produced revolutionary advances in chemical understanding, and yielded the technology to synthesize and produce useful chemicals, polymers, and medicinals; I believe that a similar focus on oxygen chemistry is appropriate and will have analogous rewards for chemistry, biochemistry, and the chemical process technologies.

NMR and computational molecular modeling studies of mineral surfaces and interlayer galleries: A review

2015 ◽  
Vol 100 (7) ◽  
pp. 1341-1354 ◽  
Author(s):  
R. James Kirkpatrick ◽  
Andrey G. Kalinichev ◽  
Geoffrey M. Bowers ◽  
A. Özgür Yazaydin ◽  
Marimuthu Krishnan ◽  
...  
Keyword(s):  
Molecular Modeling ◽  
Mineral Surfaces ◽  
Modeling Studies ◽  
Molecular Modeling Studies ◽  
Computational Molecular Modeling

Exploring Student Thinking About Addition Reactions

2020 ◽  
Author(s):  
Solaire Finkenstaedt-Quinn ◽  
Field M. Watts ◽  
Michael N. Petterson ◽  
Sabrina R. Archer ◽  
Emma P. Snyder-White ◽  
...  
Keyword(s):  
Organic Chemistry ◽  
Student Thinking ◽  
Addition Reactions ◽  
Think Aloud ◽  
Chemistry Curriculum ◽  
Student Reasoning ◽  
Chemistry Students ◽  
Resonance Stabilization ◽  
Paper And Pencil ◽  
Minimal Research

While student reasoning about many of the reaction types covered in the organic chemistry curriculum have been studied previously, there is minimal research focused specifically on how students think about the mechanisms of addition reactions. This study addresses that gap by probing organic chemistry students’ thinking using think-aloud interviews as they worked through two different addition reactions. Students worked through the mechanisms using either paper and pencil or an app that dynamically represents the molecules. Overall, students were able to identify the steps of the two addition reactions but did not always successfully apply chemical thinking during the mechanistic steps. Specifically, both groups of students struggled with the concepts related to carbocation stability, frequently misapplying stabilization via substitution and demonstrating difficulty in identifying the potential for resonance stabilization. Our results suggest that instructors should emphasize the conceptual grounding directing mechanistic steps, in particular when determining carbocation stability.

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