Achieving understanding of complicated molecular phenomena from two-dimensional drawings can be a challenge. Three examples are the C₂ and C₃ symmetry operations in chiral tris chelates, the assignment of absolute configurations in these molecules, and the non-dissociative mechanisms (Bailar Twist and Rây-Dutt) that interchange Λ and Δ enantiomers. Combining three-dimensional representations of the molecules from the Cambridge Structural Data Base, computational output examining the imaginary frequencies of transition states, and the powerful molecular visualization program Jmol, we present here a Web site to aid in teaching these concepts.

Population versus Sampling Statistics

When scientists draw random samples to be measured they expect their results will be accurate, assuming all systematic errors have been removed from the experiment. Unlike systematic errors, random errors cannot be removed from the experiment—only reduced. If several replicates are measured for each sample, random errors are mathematically minimized and are relegated to affecting precision, not accuracy. For some students, the difference between accuracy and precision is not clear enough for this to make sense. The solution is for students to interact with the statistics, which requires the laborious generation of multiple sets of random numbers, numerical comparisons, and graphical presentations of the data. The purpose of the spreadsheet exercise presented here is to remove the hurdle of constructing and generating such an interaction. The spreadsheet provides students with a self-led exercise that reinforces the statistics of sample and population distributions.

Courses in computational chemistry are increasingly common at the undergraduate level. Excellent user-friendly programs, which make the execution of ab initio calculations quite simple, are available. However, there is a danger that the underlying SCF procedure (usually coupled with contracted Gaussian atomic orbital basis sets) can become a ‘black box’ for the student. This Microsoft Excel spreadsheet contains all the essential elements of far more complicated ab initio calculations, but on the simplest possible molecular system.

In typical physical chemistry courses the student is told how the van der Waals equation works. The mathematics needed for making a Maxwell construction is difficult for the average chemistry student (what is needed are the roots of a cubic polynomial). This makes it difficult to show how the liquid–gas phase diagram is obtained from the equation of state. Here a spreadsheet experiment is presented that can be used to illustrate various aspects of the van der Waals equation of state.

SymmetryApp is a new visualization program characterized by a high level of user interactivity. Specifically, it is able to define a symmetry element anywhere in the molecule and determine the effect of the corresponding symmetry operation. This allows students to capitalize on the most important aspect of interactive learning—to make mistakes and to learn from them.

It is often necessary in general chemistry courses for students to find the best-fitting line through a set of scattered data. The method of least squares is routinely used as the statistical tool to accomplish this. However, the process behind the least-squares method, minimizing the sum of the deviations squared, is not clear to beginning students. Blind use of the analytical formulas for a slope and a y-intercept is not pedagogically effective, and it does not satisfy analytically minded students. With this in mind, we have made the process of minimizing the sum visible by allowing the individual to adjust heights in a bar graph, thus making the process more interactive and dynamic.

This interactive application presents the principles of gel permeation chromatography (GPC) for students in introductory undergraduate courses of chemistry and biochemistry. The presentation is in four sections: Introduction, Real Lab, Virtual Lab, and Microscopic Model.

This Web-based system of note cards has been developed to aid students in learning the vast number of reactions encountered in organic chemistry.

The Berry pseudorotation is a classical mechanism for interchanging axial and equatorial ligands in molecules with trigonal bipyramidal geometry. Teaching this mechanism presents particular pedagogic problems due to both its dynamic and three dimensional character. The approach taken here illustrates these processes using interactive animations embedded in a Web page and overcomes many limitations of a printed page.

Computer Simulations of Salt Solubility provides an animated, visual interpretation of the different solubilities of related salts based on simple entropy changes associated with dissolution: configurational disorder and thermal disorder. This animation can also help improve students’ conceptual understanding of chemical equilibrium before any quantitative interpretation of equilibrium constants is attempted.

3D Molecular Symmetry Shockwave is a Web-based application for interactive visualization and three-dimensional perception of molecular symmetry. The user interface is simple, and students learn how to use the program from the built-in help screens. The animation uses the Macromedia Shockwave browser plug-in, and requires a download of only 256 KB, allowing it to be used even with low bandwidth Internet connections. Its performance is comparable to a desktop application.

An Animated Interactive Overview of Molecular Symmetry is a series of Web pages designed to help instructors teach molecular symmetry. These pages combine interactive Jmol images and instructional text that allow students to examine and explore the operations and elements that give rise to molecular symmetry.

A Lattice Energy Spreadsheet is a tool that easily calculates lattice energies. It also illustrates the relation between crystal structure, coordination number, and ionic radii. A Lattice Energy Spreadsheet contains five related worksheets: Lattice Energy, MX Structure Map, Kapustinsky Lattice Energy, Directions, and Discussion.

A Self-Consistent Field Calculations Spreadsheet can help your students understand the self-consistent field (SCF) procedure, typically presented in an undergraduate physical chemistry course. The spreadsheet helps students easily perform SCF calculations on a two-electron atom and see graphically how the proper solution is obtained. It is also possible for more advanced students to apply this spreadsheet to more ambitious systems.

Kieran () Lim and William F. Coleman

Instructors and students can use this spreadsheet to quickly and easily observe how the shape of a one-dimensional vibrational potential energy curve and its associated vibrational quantum energy levels depend on the anharmonicity. This illustrates the connection between the harmonic (approximation) and anharmonic descriptions of molecular vibrations.

Cubic equations of state are widely used by chemists and chemical engineers to predict the thermodynamic properties of both pure substances and mixtures. In particular, these equations enable predictions concerning the temperature and pressure at which vapor–liquid equilibrium occurs. These two educational JavaScript programs perform calculations using cubic equations of state and, equally importantly, explain how the calculations are performed.

The relation between temperature, energy, and the properties of a material is well developed. While this relation is not clearly elaborated in most physical chemistry textbooks, these relationships can easily be included in the early part of a physical chemistry course on thermodynamics, and this interactive Excel spreadsheet can help.

Connected Chemistry is a novel learning environment for teaching chemistry, appropriate for use in both high school and undergraduate chemistry classrooms. Connected Chemistry comprises several molecular simulations designed to enable instructors to teach chemistry using the perspective of “emergent phenomena”.

Mage is a graphics program especially well suited for visualizing three-dimensional structures of proteins and other macromolecules. It is an important tool for biochemists and finds many applications in biochemistry courses. We utilize Mage to create interactive instructional graphics of potential use in a wider range of undergraduate chemistry courses, and present some of those applications here.

A Pedagogical Simulation of Maxwell’s Demon can help students better understand the statistical basis of thermodynamics. The program simulates two gas chambers with an opening between them. Students set up parameters for how the demon permits or denies passage of particles through the opening, thus decreasing the total entropy of the system.

3D Normal Modes is a Web application for interactive visualization and three-dimensional perception of the normal modes of molecular vibration, suitable for undergraduate students in chemistry. The application uses the Macromedia Shockwave plug-in and has been designed and developed especially for the Web. It has a simple graphical user interface and requires a download of only 120 KB, allowing it to be used even with low bandwidth Internet connections. Its performance is comparable to a desktop application.

The Excel spreadsheet Kinetica both simulates and analyzes kinetic data for simple rate equations of the form:

Instructors or students can generate simulated kinetic data using parameters they specify, or using parameters randomized by Kinetica. The data set that is generated may then be exported for use in exercises, homework, and exams, or may be analyzed directly within Kinetica. A kinetics data set may also be imported from an external source into Kinetica for analysis.

Fundamental aquatic chemistry concepts may be introduced in general chemistry classes by computing ionization fractions and buffer intensity of aqueous phase carbonate systems. This Excel spreadsheet may used to build graphic presentations of a titration curve, distribution diagram, and buffer intensity as a function of pH. Accompanying activities are designed to enhance the concepts of acid-base equilibrium through exploring the relationship between pK_a/pK_b, pH of the solution, ionization fractions, and buffer intensity, and to exercise students’ graphing skills.
 

Obtaining digital data from analog figures is made much easier using this Windows utility. After scanning and touching-up a figure, you can import it into SpecScan to obtain X–Y data, which can then be exported to Excel or other program for additional processing.
 

The well-known Jeopardy! game format provides an engaging, alternative exercise that can enliven teaching and learning activities. This site provides everything you need to bring Jeopardy!-based chemistry activities to the WWW.
 

A Graphical User Interface for PC GAMESS

GAMESS is a set of computational chemistry tools available free for several computing platforms. Using the set of tools described here along with the pcgRun tool provided allows these tools to be used on the ubiquitous Windows PC with a graphic interface preferred by many of us over the command line.
 

Discovery Videos
Lyubov Hoffman Laroche, Gary Wulfsberg, and Barbara Young

The use of digital video for instruction has many advantages. In many situations the only way to present some chemical phenomena is through the use of video. The two video lessons presented here are examples intended to supplement our article in the August 2003 issue of JCE.
 

Copoly: A Tool for Understanding Copolymerization and Monomer Sequence Distribution of Copolymers
Massoud Miri and Juan A. Morales-Tirado

The composition and monomer sequence distribution of binary copolymers can be complicated. Using these two linked Excel spreadsheets allows you to input data and observe the results almost instantaneously. Interpreting the distributions of n-ads (for example, triads) and sequence lengths and understanding how these key copolymer properties are related is much easier using Copoly.
 

The steady-state approximation is commonly used in enzyme catalysis kinetics calculations, but how much error does the approximation introduce? This Java applet allows you to visually determine the accuracy of the steady-state and pre-equilibrium approximations.
 

Mol4D (Molecules in Four Dimensions) is a web and Chime based molecule editor and computational interface. Visualization and interactivity are the predominant features. Computational results, based on MOPAC, are obtained within seconds and structures presented using the Chime plug in. Orbital information (in VRML format) and the selection of parameters for a linear or grid scan are options.
 

This WWW-based service for the automated animation of organic reactions we believe to be a versatile tool for teaching and learning organic chemistry. It allows the investigation of the influence of substituents of starting materials on the reaction coordinate and the energy of the depicted reaction. Starting from a list of precalculated organic reactions hydrogen atoms can be substituted by a variety of organic substituents and functional groups using the molecule editor. The new set of starting material is submitted to the calculation of intrinsic reaction coordinates that yields automatically an animation of the reaction that can be viewed with the Chime plugin.
 

Using a visual approach, this applet is designed to help students learn to solve equilibrium calculations and also to help them gain a deeper understanding of the topic. It can be used by the instructor in the classroom as equilibrium topics are introduced. Sample exercises for students are included. The text is available in both English and Spanish.
 

Calculates concentrations of principal species in solutions using JavaScript. You can specify whether "1st-year" methods or mass-charge balance methods are used in the calculations. Solutions can be chosen from the included set or you can design your own.
 

Generates energy diagrams for simple Hückel molecular orbital systems using JavaScript. You can specify the determinant or select one for a specific compound from a list.
 

Simulate the kinetics of a reaction based on its mechanism using JavaScript. The idea is to write a mechanism and, based on that, follow the course of concentrations or rates of change in concentration of reactants, catalysts, intermediates, and products over time.
 

Provides practice in learning about names and properties of chemical species. You can play this game by yourself or as a group with a moderator to work the mouse and check answers.
 

Focuses on the reasons for learning the names of compounds and ions—that by learning the names we are learning information that is immediately helpful in identifying what is going on in an aqueous solution.
 

Add-ins for Microsoft Word and Excel allow chemists who use these programs to quickly and easily format common chemistry notation.
 

An Excel workbook with built-in character tables for all common point groups helps remove some of the tedium from the linear algebra calculations needed to describe bonding and spectroscopy.
 

Novel uses of the "error-bar" feature of spreadsheet packages in the areas of enzyme kinetics, vibrational spectroscopy, vibronic spectroscopy, and mass spectrometry are discussed. It is argued that using software features for purposes that were not envisioned by the programmers fosters flexibility and innovation.
 

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Sample data are smoothed and then integrated by a function developed by the author. Integration results obtained by using different values of the function parameters are compared.
 

User data can be analyzed to determine what parameter values of the first order rate expression give the closest fit, or data can be generated using user-input values of the rate parameters and random noise levels. Statistical characterizations such as confidence limits and varience are caluclated.