The Molecular Science Project
Explorations


Jump to the following Explorations:
 
  3-D Angles K vs. Extent of Reaction
  Autoionization of Water Kinetics
  Crystalline Solids Lewis Structure and Bonding Tutorials
  Cycloalkanes: A Structural Study Methane Halogenation Animation
  Dynamic Equilibrium Organic Reaction Mechanisms
  GraphLab Phase Diagrams
  Hybridization Representations
  Introduction to Protein Structure WebSpectra

New! Cal State Fullerton's FIPSE Project
*includes automated assessment and animated tutorials*


3-D Angles

3-D Angles (small) Click image to view at full size.

Visualizing three-dimensional structures is a major hurdle for chemistry students. Compounding the difficulty, chemists use three different concepts to imply geometry, although there is no obvious geometric information in two of them. The bond angle (a geometric construct) can be known from noting either the hybridization of the central atom (a quantum mechanical construct) or the coordination number (the number of other atoms bonded to the central atom).

3-D Angles uses pattern recognition principles introduced through rapid repeated exposure to three concepts to teach students to intuitively associate the three terms together in order to be able to correctly recognize the molecular structure from limited information.

Platforms
Windows 98, Me, 2000, or XP

Current Version
2.0.1 (10/04/04)

Setup Program
3-D_Angles_Setup.exe (1.56 MB; 1,642,670 bytes)

Note: If you run 3-D Angles and the program's display appears blank, you need to obtain updated video card drivers that support the OpenGL graphics library. Send e-mail to Tim Su if you continue to have problems after you have done this.

Developer
Stephen Michael Schimpf

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Autoionization of Water

This exploration is an animation that requires the Shockwave plugin.
It works with both Internet Explorer and Netscape, on both Mac and PC.

Click here to see this animation


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Crystalline Solids

Crystalline Solids (small) Click image to view at full size.

Visualizing three-dimensional structures is a major hurdle for chemistry students. Many molecular modeling programs have been designed to assist visualizing organic structures; fewer exist for crystalline compounds. 

Crystalline Solids attempts to meet that need. The program provides easily manipulated three-dimensional models of fundamental crystal structures. Students can turn and rotate either single or multiple unit cells of any of the fourteen Bravis lattice structures. They can toggle between structures where the atoms are represented by small spheres, similar to ball-and-stick models, or large spheres, which simulate the space-filling nature of the atoms in a crystal. 

Close-packed cubic and hexagonal structures provide the additional features of studying interstitial sites/holes, or close-packed planes and slip planes. Students can place atoms in small or medium sites and turn on or off the axes between the atom in the site and its nearest neighbors, or the edges of the tetrahedron or the octahedron formed by these nearest neighbours. Visualizing packing patterns is simplified by highlighting sequential close-packed planes or slip planes. 

At UCLA the program is used routinely in general chemistry, in intermediate inorganic chemistry, in a graduate solid-state class and in a chemical engineering course. We have longitudinal evaluation data on its effectiveness in general chemistry. 

Platforms
Windows 98, Me, 2000, or XP

Current Version
2.0.1 (04/20/05)

Setup Program
Crystalline_Solids_Setup.exe (1.56 MB; 1,636,985 bytes)

Note: If you run Crystalline Solids and the program's display appears blank, you need to obtain updated video card drivers that support the OpenGL graphics library. Send e-mail to Tim Su if you continue to have problems after you've done this.

Developer
Stephen Michael Schimpf

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Cycloalkanes: A Structural Study

This exploration is a Web-based tutorial that requires the Chime plug-in.

Click here to see this tutorial

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Dynamic Equilibrium

This exploration is an animation that is accompanied by a set of worksheets which can be printed out for distribution to students.

Click here to see this animation (both PC and Mac)

Worksheets
Introduction to Dynamic Equilibrium (.pdf file, requires Adobe Acrobat Reader)
Dynamic Equilibrium Exploration (.pdf file, requires Adobe Acrobat Reader)


**A version of this exploration is also available via WebCT. WebCT is used to deliver instructions, content, and to collect student responses. Email cpr@nslc.ucla.edu for more information about this option.


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GraphLab

GraphLab (small) Click image to view at full size.

GraphLab teaches basic principles and skills for graphing. The program is divided into four lessons: scaling, drawing a "best-fit" straight line, errors, and least-squares fit.

Scaling: Requires students to set the scales for graphs in which the variables that involve direct and inverse proportions and in which the scale involves exponents. Students must provide equally spaced intervals.

Best Fit Line: Students move a line with the mouse and place it so that the best fit of the data is obtained. The slope of the line must agree within 5% of the calculated least-squares-fit line.

Errors: Scientific data can contain either random and/or systematic errors. In this lesson, students must place the line to give a best fit and then decide based on the phenomena being described what kind of errors the data contain.

Least Squares Fit: In this lesson, students draw the least-squares line by minimizing the sum of the squares of the differentials, which is shown on the screen as they place the line on the data. The differentials are also shown to provide a visual sense of the minimization. Finally, students are confronted with an "outlier" when they are drawing the least-squares line. In each section students are presented with clearly stated principles and guidelines for graphing illustrated in an accompanying graph of real data from various science subject areas. Following each new principle, students are asked to summarize and evaluate that information. This informative phase is followed by an exercise phase in which students practice the skills.

Platforms
Windows 98, Me, 2000, or XP

Current Version
4.0.1 (10/04/04)

Setup Program
GraphLab_Setup.exe (408 KB; 418,641 bytes)

Worksheets
Graphlab Description (.pdf file, requires Adobe Acrobat Reader)
Graphlab Exercise (.pdf file, requires Adobe Acrobat Reader)

Developer
Stephen Michael Schimpf

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Hybridization

This exploration is an animation that requires the Shockwave plugin.
It works with both Internet Explorer and Netscape, on both Mac and PC.

Click here to see this animation


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Introduction to Protein Structure

This exploration is a Web-based tutoria that requires the Chime plug-in.

Click here to see this tutorial

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K vs. Extent of Reaction

This exploration is a small program that must be downloaded onto your computer; only works with Excel 97 on a PC.

Click here to download this exploration (a Microsoft Excel file)

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Kinetics

WebCT is used to deliver instructions, content, and to collect student responses for this exploration.

Worksheets

Kinetics Worksheets (.pdf file, requires Adobe Acrobat Reader)
Kinetics Graphing Worksheets (Microsoft Excel file)


Send e-mail to  cpr@nslc.ucla.edu for more information about accessing this exploration.

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Lewis Structure and Bonding Tutorials

These are a series of animations that require the Shockwave plugin.
They work best on PC's using Netscape (these animations each require a download on average 1 MB in size).

Click here to see the list of animations


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Methane Halogenation Animation

This animation requires the Shockwave plug in.
It w
orks with both Internet Explorer and Netscape, on both Mac and PC.

Click here to see this animation

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Organic Reaction Mechanisms

These are a series of animations that require the Shockwave plugin.
They work best on PC's using Netscape (these animations each require a download ranging from 200 KB to 3.8 MB in size).

Click here to see the list of animations

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Phase Diagrams

This exploration is an animation that requires the Shockwave plugin.
It works with both Internet Explorer and Netscape, on both Mac and PC.

Click here to see this animation

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Representations

Representations (small) Click image to view at full size.

Chemists have developed advanced written notations to convey the structure of molecules. Although the symbolism represents only the connectivity of the atoms, these impoverished representations imply the specific geometry of the molecule.

Representations trains students to relate the notation of the impoverished drawing with the richness of the three dimensional structure of the molecule. Random presentation of a variety of impoverished drawings, typical of textbooks, are compared with three-dimensional models of rotating molecules drawn using advanced lighting and rendering techniques. The models may be correct or may include logical but incorrect interpretations of the drawing. Students identify the accuracy of the model and receive corrective feedback if appropriate.

Platforms
Windows 98, Me, 2000, or XP

Current Version
2.0.1 (10/04/04)

Setup Program
Representations_Setup.exe (1.58 MB; 1,659,818 bytes)

Note: If you run Representations and the program's display appears blank, you need to obtain updated video card drivers that support the OpenGL graphics library. Send e-mail to Tim Su if you continue to have problems after you've done this.

Developer
Stephen Michael Schimpf

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adenosine.gif (2517 bytes) WebSpectra 

This site was established to provide chemistry students with NMR spectral problems.

Interpretation of NMR spectra is a technique that requires practice - this site provides 1H NMR and 13C NMR spectra of different compounds for students to interpret. Hopefully, these problems will provide a useful resource to better understand NMR spectroscopy.

This project is supported by Cambridge Isotope Laboratories, the UCLA Department of Chemistry and Biochemistry, and the UCLA Science Challenge.

Platform
Web - Try WebSpectra now

Developers
Craig Merlic
Barry Fam

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