Understanding Medicinal Plants: Their Chemistry and Therapeutic Action
Prof. Bryan Hanson
Instructor's Resource Page for Chapter 3
The first part of this chapter is a consideration of why atoms bond in the patterns described in Chapter 2. Essentially, it is bonding theory “light.” Students with a good science background from middle and high school will breeze through this; others may struggle. If one is willing to merely accept what is said about bonding in Chapter 2, then it is possible to skip this first section. However, it is provided because many students want to know why things are the way they are, and have trouble moving on intellectually without that information. Chemists are typically very detail-oriented as well. They like to know that higher-order concepts, even if they choose to accept them rather than learn them at a deep level, can in principle be traced back through a chain of logical arguments to fundamental concepts.
The second part of the chapter considers how to predict shape and polarity from structures. The discussion of shape using VSEPR theory will be familar to better-prepared students, but most of the rest of the material will be new. Shape is discussed here as part of a logical development of concepts. However, some instructors may wish to postpone a discussion of shape until is it needed in Chapter 6 (pg 189 ff) where shape becomes relevant in the context of understanding how a molecule can interact with its target. Instructors choosing this approach will have to modify their discussion of polarity, however, to overlook the sections on how shape affects polarity (that is, VSEPR theory), and stick with the general short cuts provided.
Some students may wonder why these topics are being discussed now when they won’t be used until later – the “Why do we have to know this stuff?” inquiry. It is helpful to remind students that chemistry, and science generally, build concepts vertically, one on top of another. At the same time however, it will help greatly if you introduce the ideas of shape with a discussion of why it will be important later, and repeat this message as often as you can. This also helps to build connections between different parts of the course.Learning Objectives
- Know the definitions of atoms, molecules, elements, compounds, neutrons, protons, electrons, isotopes, orbitals, atomic number, electron configuration, lone pairs, valence, the octet rule, formal charge, conformation, Newman Projection, electronegativity, and polarity.
- Recognize that the periodic table is organized based upon the electron configuration of the elements, that families in the table have the same valence electron configuration, and that moving across a row in the table involves adding electrons and protons.
- Be able to give examples of observations that were used to construct the periodic table before its true basis was discovered.
- Be able to write electron configurations for any element in the first or second row of the periodic table.
- Know how to predict which element families tend to form ions, what the charge will be, and be able to state why ions form.
- Be able to give simple descriptions of ionic and covalent bonds.
- Be able to write Lewis Structures of single atoms as well as for molecules of varying complexity, including those with multiple bonds and formal charges, starting from a condensed formula.
- Be able to describe the principles of VSEPR theory.
- Starting from a Lewis Structure of a small molecule, make predictions about bond angles and molecular shape using VSEPR theory.
- Examine a larger molecule and predict the bond angles where requested.
- Examine selected larger molecules and give a description of the overall shape.
- Understand that single bonds impart flexibility to structures or portions of structures.
- Be able to draw sawhorse and Newman Projections of selected single bonds in a structure.
- Be able to recognize cyclohexane chair and boat structures embedded in larger, more complex molecules.
- Know the trends for electronegativity within the periodic table.
- Be able to label a polar bond using the partial charge and vector notations.
- Understand in a general way the situations in which bond dipoles will cancel each other.
- Understand how to look at a larger molecule holistically and determine its approximate polarity, and if there are regions of high or low polarity.
Teaching Ideas, Activities & Resources
If you used a molecular modeling program and physical model kits when you covered Chapter 2, their use can be expanded here with great benefit. Either type of “model” (or better, both) can be used to illustrate and explore the three basic shapes predicted by VSEPR theory, or to illustrate the overall shape of much larger molecules. For instance, models of hypercin help students appreciate that it is primarily flat, and will help them make the jump from two-dimensional drawings to predictions about the overall shape. Models of cyclohexane chairs and boats are also quite helpful in deepening students’ understanding of these concepts.
Most molecular modeling programs are capable of animating rotations around single bonds to illustrate the flexibilty of single bonds. Examples of these are available from the course web site. Molecular flexibility is also readily demonstrated using a model kit. In addition, some molecular modeling programs are capable of calculating the molecular dipole moment and displaying it. Careful choice of examples may help students see how dipole vectors may cancel or partially cancel. For instance, the series of ortho-, meta- and para-dibromobenzene, being two-dimensional, are good molecules to discuss.
A useful way to introduce the idea of Newman Projections is to put the front and back atoms on separate pieces of transparency material, and use a brad to link them together at the center. The upper sheet can be rotated while the assembly is on an overhead projector. Students will then have a better sense of what is going on when the usual Newman Projections are illustrated on the blackboard. See A. E. Ciolino et al Journal of Chemical Education vol. 78 no. 10 pg. 1358 (2001).
To talk about polarity and keep student's attention, you could bring in hot water and a tea bag and discuss the process that is occuring as the tea steeps. This may sound too simple to be useful, but it really can be a springboard to good discussion. Another item to consider is some kind of herbal cream (I use the capsaicin products intended to treat joint pain), and discuss why this particular chemical comes as a cream in petroleum jelly and not as an aqueous solution.
- Periodic Tables on the web. The Periodic Table of the Elements was intrinsically ready for the web when Mendeleyev published it, and many creative and useful sites about it exist. Yahoo's page on the Periodic Table will lead you most of them. Here is a worksheet that requires students to use some of these web resources.
- Worksheet on drawing expanded structures (Lewis Strutures) from formulas and calculating formal charges.
- Worksheet on estimating polarity and polarity concepts.
- Review for Exam 1 (note: in Spring 2006 I decided to hold discussion of VSEPR and shape until later in the semester, so this exam does not cover that material).
The background on this page is a 19th century woodcut of Phytolacca americana.
Last updated Thursday, September 1, 2011 . Contents & layout copyright 2011 Prof. Bryan Hanson