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Inorganic Molecules: A Visual Database was created as tool for instructors to use in class rather than for direct student use. It includes several options that are more appropriate for use with students in an Inorganic Chemistry course rather than students in an Introductory Chemistry Course.

• Using the Discovery Questions
• Ideas for use in Lecture
• About the CAChe Molecular Modeling Molecule Files
• Inorganic Molecules on the General Chemistry Collection

Many questions require the examination of several molecules. It is most appropriate to use the Compare button to look at two molecules simultaneously.

Some of the Discovery Questions contain superscripts and subscripts. In order to see these you must install the font, JCEChem included in the installation folder on the CD.

Lecture 1: Introduction to Chemistry

In a brainstorming session on the definition of chemistry, give a framework of terms such as: composition, structure, properties, reactivity, and energy changes. A simple demonstration with Alka-Seltzer could be used to get students to identify two compounds (water and carbon dioxide) and begin thinking about their properties. Have the students list anything at all that they know about these two molecules and put their data in the context of the terms above. At the end, very few items, if any, will be listed in the category of structure.

Now introduce the two molecules from the database. Show various views of the molecules as time allows. Compare and contrast water with carbon dioxide, considering especially the shape of the molecules (molecular geometry.) Complete definitions of terms are not necessary at this time but, the demonstration gives students a preview of some of the things they will learn in the course.

Lecture 2: Elements, Atoms, Molecules

Define the terms element, atom, and molecule. As examples of molecules, consider molecules in the air: nitrogen, oxygen, and others such as: carbon monoxide, nitric oxide as time permits. Compare the models in the database to ideas of atoms of nitrogen, oxygen, and carbon. Consider allotropes of oxygen by comparison of oxygen molecule and ozone. What other molecules contain these atoms? Show some examples in the database.

Lecture 3: Law of Definite Composition and Law of Multiple Proportion

Compare and contrast water with hydrogen peroxide using ball/stick model and molecular geometry. If time permits, look at carbon dioxide with carbon monoxide. Note that molecules must contain whole numbers of atoms, and that addition of a single atom drastically changes the molecular shape and the macroscopic properties of the substance.

Lecture 4: Empirical, molecular, and structural formulas

Compare the structures of ethane, ethylene, ethyne.

Lecture 5: Name and formulas of compounds--polyatomic ions

Look at carbonate, bicarbonate, nitrate, nitrite, sulfate, sulfite, hydroxide, and ammonium ions. Have students discover the pattern in nomenclature by examining models of the molecules.

Lecture 6: Writing and balancing chemical equations

Look up the structures of the compounds used in the example of chemical reactions you use to introduce the writing and balancing of chemical equations. A couple of simple examples are:

• hydrogen plus chlorine to make hydrogen chloride;
• sulfur plus oxygen to make sulfur dioxide or sulfur trioxide.

Looking at models, you can emphasize that changing subscripts would change the molecule, you can only have whole number of molecules or atoms involved in the reaction, and that the number of atoms of each element in reactants must equal the number of atoms of that element in the product.

Lecture 7: Atomic Structure

Go to the Molecular Orbital sub menu and click on Atomic Orbitals. Examples of s, p, d, and f orbitals are given with electron density contours and animations of three dimensional models of the orbitals.

Lecture 8: Periodic Trends

Use the series nitrogen, oxygen, fluorine with covalent and van der Waals radii to see the trend in atomic radii as one moves across a row in the Periodic Table. Also compare some group trend molecules such as ammonia and phosphine, water and hydrogen sulfide, hydrogen chloride and hydrogen iodide.

This may also be the right time to look at bond lengths and also to use the Visual Info menu to find definitions terms that are new to the class.

Lecture 9: Covalent Bonding

Although there is not a specific section in the database that addresses formation of covalent bonds, there are images that can be used to enhance a first simple approach to covalent bonding.

From the Visual Info menu select Molecular Orbital (M.O.) Theory. Click the buttons below the introductory text to display text and graphics describing the interaction of the hydrogen atoms s orbitals to form a bonding molecular orbital (overlap).

From the Molecular Orbital Diagram menu select M.O. Energy Diagram

Click the lowest energy M.O., sigma-s. Click the three buttons on this card in turn to show the overlap of two s orbitals. Return to the M.O. Energy Diagram by clicking the bent arrow.

Click the sigma-px orbital line and again look at all three buttons to show how two px orbitals may overlap, (head on). Return to the M.O. Energy Diagram by clicking the bent arrow.

Select πpy or πpz to illustrate simple π bond formation (side by side overlap). Return to the M.O. Energy Diagram by clicking the bent arrow. Return to the Molecular Orbital menu by clicking the Menu button.

Click Hydrogen Chloride and then click M.O. 2 to see a simple s and px orbital combinations.

At this point you could look at some of these same combinations for specific molecules such as oxygen and nitrogen. At the first introduction, it is not necessary to proceed further into molecular orbitals including antibonding orbitals. More complete M.O. theory, if addressed in the course, should be reserved for later.

Lecture 10: Lewis Diagrams

Just about any molecules that you use to introduce Lewis diagrams can be shown. Click the name of the molecule or ion from the molecule selection menu. Click the Model button to show a Ball/Stick and Lewis diagram. This may also provide a means to show a series of related molecules very quickly such as: ammonia and phosphine, water and hydrogen sulfide. Because the ball/stick models are also available along with a three dimensional animation, you may wish to begin introduction of molecular geometry at this time.

Lecture 11: Lewis Diagrams and Resonance

Included in the database are several series of compounds that would provide a good introduction to resonance.

For example compare the structures of carbonate, bicarbonate, carbon dioxide, carbon monoxide, and formaldehyde. Explore the ideas of resonance, bond order, and bond length and also look for the definitions of these terms in the Visual Info menu.

Some discussion questions for students are: Is there a direct correlation of bond length and bond order? How does the concept of resonance help to answer this question?

Lecture 12: Polar and nonpolar molecules

Compare a simple series of diatomic molecules to discover which of these are polar and which are nonpolar. (Click the Dipole button on a molecule card.) Ask students to describe the major difference between the two.

Also consider electronegativity differences.

Next compare carbon monoxide with carbon dioxide. Why the difference in polarity? Also compare boron hydride with ammonia; and ammonia with nitrogen fluoride; boron trichloride with phosphorus trichloride.

Lecture 13: Polarity and Electrostatic Potential

For a more advanced presentation check out the Visual Info for the definitions of polarity, electronegativity, relative partial charges, and electrostatic potential.

Lecture 14: Molecular Geometry

There are many approaches to using the data base for the differences between electron pair geometry and molecular geometry. From the Optional Views menu, you can also activate a hybridization identification of various atoms in molecules.

Refer to the section Questions Based Upon The Molecule Comparison Sets for ideas on how to use this for the section on molecular geometry. The questions work well for group discussion or for student assignments.

Start out slowly by comparing the electron pair geometry and molecular geometry in triatomic molecules. Why are some bent and some linear?

Gradually work up through tetraatomics such as ammonia, boron hydride, boron trichloride, sulfur trioxide, etc.

Finally look at those based on tetrahedral, trigonal bipyramidal, and octahedral electron pair geometries.

The database should be very useful in this area for all kinds of comparison questions, discovering the rules for various geometries, relating to hybridization, and student homework assignments.

Lecture 15: Equilibrium

Most textbooks include a discussion of the classic demonstration experiment involving nitrogen dioxide and dinitrogen tetraoxide. Some new insights into this equilibrium may be gained by comparison of the two molecules covalent radii, van der Waals radii, bond lengths, resonance structures, bond order, and electron pair and molecular geometry. These molecule views show that in dinitrogen tetraoxide N--N bond length is abnormally long for a single bond, which corresponds to the fact that the bond order is about 0.5. The bond is longer than the sum of the van der Waals radii. It might also be useful to look at the HOMO of both molecules to see the orbital overlap.

Lecture 16: Acids and Bases

The database includes several binary acids (HCl, HI, and hydrogen sulfide), quite a number of simple oxy-acids (nitric, nitrous, sulfuric, sulfurous, carbonic, bicarbonate ion, and phosphoric acid), and the hydronium ion as well as several bases including ammonia, phosphine, and hydroxide ion. These can be used to illustrate various examples of acids and bases. The Lewis structure/Resonance graphics for hydronium ion illustrate two views of a four water/hydrogen ion coordinated ion.

Lecture 17: Molecular Orbital Theory

If you introduce Molecular Orbital theory in general chemistry, students may be able to understand more easily with the visualizations possible from the Molecular Orbital Diagrams menu. Complete descriptions are available for atomic orbitals and the molecular orbitals of fluorine. The orbitals are described with a plane contour surface, three dimensional plane contour surfaces, and finally the orbital isosurface with animation.

Further descriptions of M.O.'s are given in the Visual Info menu including some simple theory, color coding, HOMO, LUMO, and Density color by HOMO and LUMO. The information included here will not be a sufficient introduction for general chemistry students, but it should be a useful addition to your text and other instructional materials.

Complete molecular orbital diagrams are given for seven diatomic molecules, and ammonia, water, and carbon dioxide. Each molecular orbital is available in two views including one with the wave function shown.

Lecture 18: Lewis Acids and Bases

For more advanced applications, enable the "M.O. Reaction Predict" option from the "Optional Views" menu. Review the descriptions in the "Visual Info" menu: M.O. Reaction Prediction, HOMO/LUMO, and LUMO/HOMO. This gives instructions to use the molecular orbital features to predict reactions of Lewis Acids and Bases.

Lecture 19: Air Pollution Molecules

A discussion of any of the popular topics will be more complete if you illustrate the molecules using the database.

Ozone Depletion: oxygen, ozone, chlorine monoxide, hydroxyl radical, chlorine, hypochlorous acid, nitric acid, (sorry no example of a CFC is available).

Global Warming: carbon dioxide, methane, nitrous oxide

Acid Rain: sulfur dioxide, sulfur trioxide, sulfurous acid, sulfuric acid, nitric oxide, nitrogen dioxide, nitric acid, nitrous acid

Photochemical smog: carbon monoxide, ozone, hydroxyl radical, nitric oxide, nitrogen dioxide, methane, ethane

The files in the CAChe files folder were used in the development of Inorganic Molecules: A Visual Database. You must have the CAChe Scientific Molecular Modeling program or some other molecular modeling program that can read CAChe files in order to open and use them. The steps below outline the process used to create the images in the database.

1. The molecules and ions were made in the Editor and the geometry optimized using MOPAC PM3 (with only a few exceptions).
2. For most of the structures, the models were then modified by hand in the Editor using literature values for bond length and bond angles. If literature values were not available, then the original PM3 results were used for the molecular orbital calculations.
3. MOPAC PM3 was again used with SCF (self consistent field) energy calculations to obtain results for the molecular orbital calculations.
4. The Tabulator was used to obtain the molecular orbitals and density color by electrostatic potential. Most of these files are contained in the folders. Other Tabulator calculations may be run since the source file folder is included.

The version included on the General Chemistry Collection CD-ROM includes the Discovery Questions but does not include the CAChe Molecular Modeling Molecule Files that are found on the Inorganic Molecules: A Visual Database CD-ROM.