unitsHome

If you have difficulty accessing or playing units, please email the author (woodmandj@aol.com) with details of the problem, your computer type and operating system, and browser and version. Work is in progress on some problems reported in various browsers with Mac OSX

The Chemistry Teaching Graphics Concept Unit s are a collection of computer presentations with audio and animation, using 3D molecular and other models - on topics where computer graphics may be helpful in depicting dynamic processes, complex 3D structure and relationships, and the microscopic molecular view of matter - chemistry learning resources for classroom projection or individual tutorial study.

(For a separate collection of computer graphics based chemistry Interactive Exercises and chemistry multiple choice Sample Exam questions, many on the same topics as the units below, go to: Interactive Exercises which is a subset of the larger student web study materials collection found at: webExHome )

Computer Set-Up: Display screens (640x480) work best in an 800x600 (or larger) window - or use the Opera browser true full-screen display with 640x480 resolution. Many units require thousands or millions of colors. QuickTime needs to be installed. First time users will be prompted to download and install the Shockwave plug-in.

To play a unit, click on its title below. To progress through a unit, click on the light green (or light blue) buttons in the upper right corner of the screen. AUDIO: Audio plays on many screens when they are accessed by the colored buttons. (Sound does not play automatically when screens are accessed by arrow buttons or by the Navigator menu.). A speaker icon at the top center of a screen plays or replays the audio for that frame. Volume can be adjusted (or muted) with the Audio menu. MOVIES: Light blue buttons in the upper right corner of a screen designate QuickTime movies, which may require a minute or so to download (with fast web connections) before playing. Several minutes may be required to download movies via slower phone modem connections before movies will play. In most cases a red sign will warn when movies are still loading. A control slider at the top of the movie screens can be used to adjust the movie rate.

Problems, comments and suggestions should be sent to Darrell J. Woodman at woodmandj@aol.com.

YOUR PATIENCE IS APPRECIATED DURING TEMPORARY SHUTDOWNS AS IMPROVEMENTS ARE BEING MADE.
YOU MAY NEED TO CHANGE BROWSER BOOKMARKS AS SOME REVISED UNITS ARE MOVED.

ORDER OF LATEST ADDED UNITS: Ethane Rotation, SN1 Stereochemistry(SEE SPECIAL INFO BELOW), SN2 Inversion, SN2 Mechanism, SN1 Mechanism, E2 Mechanism, Balancing Equations - Revised, Limiting Reagent, Percent Composition-Molecular Formula, Law of Multiple Proportions, Hydrogenation, Work: Gas Expansion, Haworth Formulas, Photoelectric Effect, Propane, Buffering, RSnaming, Tetrahedral Stereocenter, Pleated Sheet/Silk Fibroin, tRNA, DNA, Nucleophilic Addition to a Carbonyl, Waves1D2D3D, ForcesBranchingBP, IonForces, ForcesDipolesH-bonding, Diatomic Molecular Orbitals, Benzene Resonance, VSEPR (sound verson), Acid Base, Covalent Bond, ChemPhys Change, Myoglobin, Elements

The recently added unit "SN1 Stereochemistry" is a test of a new format to eliminate problems with Quicktime movies not playing properly on both older and newer computers, especially on the Mac side. (It is necessary to have Quicktime installed.) If this new version doesn't play the movies (blue buttons), please report that to me, with information regarding the computer and browser you are using. An alternative, older version of this unit can also be tested for comparison, by changing the browser toolbar address from "....w2.html" to "...w.html".

The previous work-around for the movie-play problem (and other new problems) in Mac OS 10.4 with many browsers, whether or not they are set to open in Rosetta was to try instead, Internet Explorer version 5.2 for Mac (available for free web download).

Structure and Bonding

Elements   Microscopic/atomic scale introductory view of the structure of various types of elements. Static graphics, no animation. Intended as a prelude to the companion unit "ChemPhys Change."

Law of Multiple Proportions   Uses hypothetical compounds between "boltium" and "nuttigen" to illustrate ratios of atomic ratios and ratios of elemental weight ratios and the Law of Multiple Proportions.

Percent Composition - Molecular Formula   Uses hypothetical compound between "blueium" and "greenon" atoms to illustrate calculation of empirical and molecular formulas.

Nuclear Size  Zoom animation relating the size of the nucleus of an atom (of ~ 100 pm radius) to the size of a marble on home plate of a ballfield (of ~ 100 m radius).

Probability Distribution Depicts 1s electron probability distribution through animated development of a rotating 3D dot density plot, and animated generation of 3D orbital sphere.

Aufbau Illustrates electron-filling in the periodic table through the 4s and 3d subshells. For quick class examples or problems, clicking on any element goes directly to its display. Alternatively, "fill subshell" buttons provide quick animations showing the spin of each electron as it moves to its orbital. (Requires 38 movies in the same folder.) For more emphasis on the orbital and spin choices, "individual electron" or forward arrow buttons can be used to examine these choices more slowly in steps.

Covalent/Ionic Bonding Animations of formation of covalent, polar covalent, and ionic bonds.

Covalent Bond Animations of the energy change as two hydrogen atoms approach to form a covalent bond. Compares electron cloud, space-filling (90% boundary surface), transparent boundary surface, covalent radius spheres, wave function, and schematic atom representations of bonding.

Photoelectric Effect Aninmations of photoelectric effect, (varying light beam intensities and frequency) with discussion of theory, followed by animation of photon absorption and summary of energetics..

Waves 1D 2D 3D   Aninmations of waves and nodes in one, two, and three dimensions.

Molecular Orbitals   An examination of the bonding and antibonding combinations of s and p orbitals.

Diatomic Molecular Orbitals   Depiction of overlapping atomic orbitals, resultant bonding and antibonding molecular orbitals and electron configurations for homonuclear diatomic molecules of hydrogen through neon.

VSEPR Geometries Inflating balloons demonstrate the successive VSEPR geometries. Will students predict the ourcomes?

SP3 Hybridization Animation of the formation of sp3 hybrid orbitals, using orbital phase colors of superimposed atomic orbital combinations to clarify the the hybrid orbital geometries.

SP2 Hybridization Animation of the formation of sp2 hybrid orbitals, using orbital phase colors of superimposed atomic orbital combinations to clarify the the hybrid orbital geometries.

SP Hybridization Animation of the formation of sp hybrid orbitals, using orbital phase colors of superimposed atomic orbital combinations to clarify the the hybrid orbital geometries.

Benzene Resonance Animation of the delocalization of a hypothetical 1,3,5-cyclohexatriene (with energy curve), animated orbital views, pi circle representation, and contributing structure views.

Solids - Crystals

Close Packing Detailed comparison of cubic and hexagonal close packing patterns. All views rotate. Preliminary no-audio version.

Ionic Crystals Shows CsCl, NaCL, and ZnS lattices with framework models (unit cells and 8 cell aggregates) and space filling models (including "sliced atom" views of unit cells), showing cubic, octahedral and tetrahedral holes. All views rotate. Preliminary no-audio version.

Intermolecular Forces and Physical Properties

Intermolecular Forces Illustrates different types of forces between molecules (ion, dipole, induced dipole, and London forces), with a "race" to compare magnitudes.

Ion Forces Animated approach of sodium and chloride ions with energy graph.

Forces: Dipoles, H-bonds Molecular dynamics animation showing H-bonding dipole attraction causing HF molecules to coalesce into a microdroplet.

London Forces Animated simulation of transient and induced dipoles, followed by comparisons of stabilization energies for different approaches of two nonpolar chlorine moecules.

States of Matter Short molecular dynamics animations (unshaded graphics) of molecular motion in the solid phase (simple cubic lattice of 64 diatomic hydrogens), on melting, in the liquid phase, on vaporization, and in the vapor phase.

Forces: Branching, Boiling Point Low temperature molecular dynamics animations comparing unbranched pentane with the highly branched isomer neopentane. Favored parallel orientation for n-pentanes is evident in a comparison with pairs of each molecule. With four molecules of each type the lesser London Force attraction for the spherical neopentanes is reflected in less clustering than for pentane..

Oil & Water Molecular dynamics microscale animation of the separation of mixed methane and water molecules.

Like Dissolves Like Molecular dynamics animations with microsamples of 5 different solute-solvent combinations to illustrate that solubility results when solute-solvent attractive forces are competitive with both solute-solute and solvent-solvent attraction.

.

Thermodynamics

Work: Gas Expansion Derivation of the equation W(surr) = P(ext) x DV - using animations of a gas in a cylinder (cutaway view) with a piston and of the particulate view of internal and external forces.

Ethane Rotation Animations of rotation of space filling ethane molecule and interconversion of different staggered and eclipsed views of both space filling and ball stick models. Definition of (torsional) energy barrier to rotation and Newman projection formulas. Animated generation of energy graph vs dihedral angle. M.O. explanation of energy difference between eclipsed and staggered conformations.

Propane Space filling model animations of the the interconversion of propane conformations, showing the two-dimensional conformational energy surface and an explanation of the extra destabilization of the di-eclipsed conformer.

Chair Cyclohexane Illustrates puckered chair cyclohexane ring with animations of turns from top to side and end views, color coding of equatorial and axial hydrogens

Chair Chair Interconversion Animation of the interconversion of chair conformations with a tour through intervening half-chairs, twist-boats, and a boat. Preliminary no-audio version.

Tetrahedral Stereocenter Animation of a tetrahedral stereocenter looking in a mirror to see its mirror image, followed by two unsuccessful attempts at superposition. Then a second mirror is used to show that any mirror generates the same mirror image.

RSnaming Builds a color-coded priority table and model for the textbook example 2-butanol, then animates turns to side and back views of model for classification.

ChemPhys Change Microscopic/atomic scale comparison of chemical vs physical change. Static graphics, no animation. Intended to follow the companion unit "Elements"

Balancing Equations - REVISED Uses a 3D graph of integers (spheres) to illustrate balancing an equation (water formation) by finding the smallest non-zero integer solution to the two simultaneous mass-balance (or atom-balance) equations for the elements. Revised version with audio and comparison of the method of sequential coefficients..

Balancing Equations Uses a 3D graph of integers (spheres) to illustrate balancing an equation (water formation) by finding the smallest non-zero integer solution to the two simultaneous mass-balance (or atom-balance) equations for the elements. Preliminary no-audio version - SLATED FOR REMOVAL IN SEPT.

Limiting Reagent Illustrates the use of reactant ratios to determine the limiting reagent or reactant and shows the calculation of percent yield.

Reaction Coordinate Animation of the formation of 2HI by the collision of a hydrogen molecule with an iodine molecule, to illustrate energy changes (heat of reaction and activation energy) in a chemical reaction.

Acid Base Introduction to model animations of the mechanistic curved arrow notation and the rule that "a stronger acid forms a weaker acid.

Buffering Contrasts changes in hydronium ion concentration and pH when acid is added to water and to a buffer solution.
.

Organic Reactions and Mechanisms

Hydrogenation Animation of the mechanism of catalytic hydrogenation of cyclopentene using the isotope deuterium to illustrate the stereochemical course.

E2 Mechanism Animation of the mechanism of E2 elimination, comparing the anti coplanar transition state geometry with the syn alternative and showing the energy profile and rate expression.

SN1 Mechanism Animation of the SN1 mechanism, including orbital and charge-gradient views.

SN1 Stereochemistry Animated summary of the stereochemical outcome of the SN1 mechanism, using parallel pathways with both achiral and chiral alkyl halides. NEW VERSION TEST - SEE ABOVE.

SN2 Mechanism Animation of the SN2 mechanism, including orbital and charge-gradient views.

SN2 Inversion Animation of Walden inversion in the SN2 mechanism.

Benzyne Animation of the mechanism of the formation of benzyne and its reaction with ammonia, using both models (with orbital views) and formulas.

Epoxidation  Animation of the peracid epoxidation of alkenes using formulas to show the traditional "butterfly" transition state and with both space-filling and ball and stick models to show the newer proposed spiro geometry

Aromatic Substitution  Animation of the mechanism of electrophilic aromatic substitution, using both models (with orbital views) and formulas.

Nucleophilic Addition to a Carbonyl Animation of the mechanism of base-catalyzed addition of water to acetaldehyde.

Enolate Anion Animation of the base catalyzed conversion of a carbonyl to an enol, including orbital views.

Acyl Substitution  Animation of the mechanism of nucleophilic acyl substitution, using both models (with orbital views) and formulas.

Haworth Formulas Line-bond animations of the puckering of the Fischer projection formula of D-glucose, rotation about the C4-C5 bond, cyclization, and conversion to the stylized Haworth sugar formulas for the a- and b-pyranoses, followed by puckering to chairs..

Nylon Animations 1) zoom in on an extended chain to show the repeating unit and 2) show two segments aligning to form hydrogen bonds.

Protein Primary Structure The first in a series of units that tour the levels of protein organization. Here a space-filling model of bovine insulin changes to a display of spheres to represent each amino acid (color-coded by polarity, acidity, and basicity). The spheres model of the globular molecule unwinds to show the primary structure of the chains - with a box to toggle on and off displays of three-letter and one-letter abbreviations for the amino acids.

Protein Secondary Structure The second in a series of units that tour the levels of protein organization. One example each is given of helices (with winding animation from fully extended chain), sheets (with puckering animation) and bends (with coiling animation). Multiple rotating displays.

Pleated Sheet, Silk Fibroin Animated depiction of puckering fully extended chains to form H-bonds, association of antiparallel chains in pleated sheets, and stacking of sheets in the 3rd dimension.

Protein Tertiary Structure The third in a series of units that tour the levels of protein organization. The helical segments bent into the globular tertiary structure of myoglobin are shown with space-filling, backbone, and ribbon models. Then one example each is given to illustrate motifs and domains. All displays rotate.

Myoglobin Examines factors involved in tertiary protein structure for myoglobin by color hi-liting of first (external) polar side chains and the distribution of charged polar groups on the protein surface, then (internal) nonpolar side chains. Polar side chains are cut away for a better view of the nonpolar interior groups. Next all side chains are cut away showing color hi-lited prolines helices terminating helical sections. A further display hi-lites interhelix H-bonding or salt bridges. Finally the carbonyls are removed to emphasize the helical backbone. Most displays rotate.

Protein Quaternary Structure The fourth in a series of units that tour the levels of protein organization. An animation shows the approach of the four, differently colored subunits of human deoxyhemoglobin. Then ribbon and space-filling models both rotate. Next, as one example of the extended secondary structures of a fibous protein, a series of dissolves lead from a glypropro sticks model to a left-handed helix, then on to the superhelix of a collagen microfibril (coils, sticks, and space-filling models, all with differently colored subunits). For another fibrous example, see the separate unit "Pleated Sheet" (silk fibroin).

DNA Examination of a 12 base-pair segment of synthetic DNA (1). Ball-stick and space-filling displays rotate to emphasize the major and minor grooves. The two strands are shown in different colors and separated, noting the right-handed helicity. A wire-frame display is used to show that the chains are antiparallel. The sugar-phosphate backbone is also shown separately. In case it is desired to cover or review base pairing in this unit, there is provided a final section that shows the base pairs (color coded by type) and restacks the double helix.

tRNA Examination of models of yeast phenylalanine tRNA, including rotation of wire frame view and zoom animations of acceptor stem and anticodon - both also shown as space filling.

Citric Acid Cycle (or Krebs Cycle or Tricarboxylic Acid Cycle) An overview of the citric acid cycle (with options to show compound or enzyme names) includes a cycle animation, which uses red spheres to depict the repetitive catabolic conversion of acetyl-CoA to two carbon dioxides. Next a sequence of simplified schematic mechanistic animations of the reactions of the citric acid cycle reconstruct the summary screen. A series of dissolves then depicts the distribution of isotopic labels from the methyl carbon and from the carbonyl carbon (either separately or combined) of acetyl-CoA. Subsequent displays show free energy changes, regulation points, controls, inhibitors, activators, anabolic pathways, and anaplerotic reactions. Preliminary, no-audio version.