Information • Textbooks • Media • Resources edited by
JCE Software
Jon L. Holmes Nancy S. Gettys University of Wisconsin–Madison Madison, WI 53706
Advanced Chemistry Collection
W
Abstract of Special Issue 28, a CD-ROM (for Students) The JCE Software Advanced Chemistry Collection CDROM for Mac OS and Windows contains software for advanced undergraduate chemistry students (those in courses beyond the general or introductory level, such as organic chemistry, analytical chemistry, physical chemistry, or special topics courses).1 The CD includes both previously published and new peer-reviewed software on a single CD-ROM for convenient access by students. The programs included on this CD-ROM and the topics they address are listed in Table 1. Abstracts for the two programs not previously published by JCE Software are below. The Advanced Chemistry Collection is modeled on the General Chemistry Collection (1), now in its 4th edition. Students will find the programs in the Advanced Chemistry Collection useful tools for learning chemistry outside the classroom as they progress through the chemistry curriculum. Hardware and Software Requirements General requirements are given in Table 2. Some programs have additional special requirements. Please see the individual program abstracts (http://jchemed.chem.wisc.edu/ or previous issues of JCE), or documentation included on the CD-ROM for more specific information. Acknowledgment This CD-ROM contains the work of many authors. The time and effort of these dedicated chemistry educators is gratefully acknowledged by the editors, along with the authors’ generosity in contributing their work to the chemistry education community by submission to JCE Software. Thanks are also due the many peer reviewers who volunteered their time to test these programs, and the thousands of chemistry instructors all over the world who have made these programs available to their students. Their input has been invaluable in program development, revisions, and updates. Licensing and Discounts for Adoptions The Advanced Chemistry Collection is intended for use by individual students. Purchasers are licensed to install and use the software on a single computer only. Installation onto network servers or computers used by more than a single individual is strictly forbidden. Institutions and faculty members may adopt Advanced Chemistry Collection as they would a textbook. We can arrange to package CDs with laboratory manuals or other course materials or to be sold for direct distribution to students through the campus bookstore. The cost per CD can be quite low (as little as $3) when large numbers are ordered, making this a cost-effective method of allowing students access to the software they need whenever and wherever they desire. Other JCE Software CDs can also be adopted. Contact us for details. 1526
Table 1. Contents of the Advanced Chemistry Collection Software for Mac OS and Windows
Topics
Alkanes in Motion
Molecular models, Molecular motion, Molecular vibration
Enriching Quantum Chemistry with Mathcad
Quantum chemistry, Mathcad
Group Theory with Mathcad
Group theory, Mathcad
Schroedinger.m
Quantum chemistry, Mathematica
Solid State Structures
Solid state, Structural chemistry
Software for Mac OS
Topics
Acid–Base Package
Titration curves, Buffers, Alpha plots
Coordination Compounds
Octahedral complexes, Structural isomers, Inorganic nomenclature
Frost Diagrams: A Tool for Predicting Redox Reactions
Oxidation–reduction, Frost diagrams
MacMS: A Mass Spectrometer Simulator
Mass spectrometry
Molecular Dynamics of the F+H2 Reaction Reaction dynamics MolVib 2.0
Molecular vibrations, Normal modes
Organic Nomenclature
Organic nomenclature
Pericyclic Reactions: FMO Approach
Pericyclic reactions, Molecular orbitals
Precision of Calculated Values
Experimental error
Proton NMR Spectrum Simulator
NMR
PTRJ
Kinetics, Theoretical chemistry
Reaction Dynamics
Reaction dynamics
Symmetry Elements and Operations
Symmetry
Viscosity of Polymer Solutions
Density, Polymers
Software for Windows
Topics
Buffers Plus
Alpha plots, Buffers, Titration curves
DYNAM: Molecular Dynamics Simulator
Molecular motion
Enzyme Lab
Enzymes, Reaction rate
Equilibrium Calculator
Equilibrium calculations
G and S GC Instrument Simulator
∆H, ∆S, ∆G calculations, Entropy Gas chromatography
HIPPO-CNMRS HPLC for Windows
NMR Chromatography
Simulation of the Physical Chemistry of Gas Chromatography
Gas chromatography
SPECPNMR
NMR
TorAD for HyperChem/Excel
Molecular motion, Rotation about torsional angle
Viscosity Measurement
Density, Viscosity
WinDNMR: Dynamic NMR Spectra
NMR
Window on the Solid State: Parts I–IV
Solid state
Winspec: Microwave Spectroscopy Tutor
Microwave/rotational spectroscopy
Journal of Chemical Education • Vol. 77 No. 11 November 2000 • JChemEd.chem.wisc.edu
Information • Textbooks • Media • Resources
MacMS: Mass Spectrum Simulator (Mac OS)
GC Simulator (Windows)
Price and Ordering An order form inserted in this issue provides prices and other ordering information. For additional information, contact JCE Software, University of Wisconsin–Madison, 1101 University Avenue, Madison, WI 53706-1396; phone; 608/ 262-5153 or 800/991-5534; fax: 608/265-8094; email:
[email protected]. Information about all our publications (abstracts, descriptions, updates) is available from our World Wide Web site, http://jchemed.chem.wisc.edu/JCESoft/.
WinDNMR (Windows)
Note 1. Previously published software from our MS-DOS series is not included on Advanced Chemistry Collection. It is now available for free download by JCE subscribers. For more information go to http://jchemed.chem.wisc.edu/JCESoft/.
Literature Cited 1. General Chemistry Collection, 4th Ed.; J. Chem. Educ. Software, 2000, SP16.
Table 2. General Hardware and Software Requirements for the Advanced Chemistry Collection
Computer
CPU
RAM
Drives
Graphics
Operating System
Mac OS Compatible
68040 or higher, Power Mac suggested
≥ 16 MB
CD-ROM; Hard Drive
≥ 256 colors; ≥ 640 × 480
System 7 or higher
Acrobat Reader (included); Mathcad; Mathematica; MacMolecule2; QuickTime 4; HyperCard Player
Windows Compatible
80486 or higher, Pentium suggested
≥ 16 MB
CD-ROM; Hard Drive
VGA; SVGA with ≥ 256 colors; ≥ 800 × 600
Windows 98/95
Acrobat Reader (included); Mathcad; Mathematica; PCMolecule2; QuickTime 4; HyperChem; Excel
Other Software (required by one or more program)
Advanced Chemistry Collection
PTRJ Alexander Grushow Department of Chemistry and Biochemistry, Rider University, Lawrenceville, NJ 08648-3001
PTRJ, for Mac OS, was devised as a tool to help students develop an understanding of the relationship between reactions on the microscopic and macroscopic scales through the use of a reaction potential energy surface (PES). PTRJ includes five potential energy surfaces based upon the one developed by Porter and Karplus (1) for the H + H2 reaction. For each PES, the user can choose an initial state of the system and then calculate a classical reaction trajectory and find the final state of the system after the trajectory leaves the bounds of the surface. An animation of three atoms appears at the bottom of the screen as the path of the trajectory is plotted on the PES. This visualization in direct conjunction with the plot of the trajectory path allows students to quickly become expert at visualizing the motions of the atoms on the PES.
This screen from PTRJ shows a the result of a trajectory.
JChemEd.chem.wisc.edu • Vol. 77 No. 11 November 2000 • Journal of Chemical Education
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Information • Textbooks • Media • Resources
Because of its complex nature, a PES is difficult to discuss in a lecture setting. However, this same aspect facilitates experimentation in a discovery-style setting. PTRJ can be used as a guided laboratory exercise in which students observe the effects of initial conditions on the trajectory outcome. While they may not completely understand the mechanics behind the calculation of the trajectory, they are able to interpret the motions of the atoms on the PES in a way that introduces them to the concept of a reaction on a microscopic scale. Using leading questions, students are also able to begin to understand the relationship between microscopic and macroscopic reactions. PTRJ’s documentation includes an introduction to the concept of a reaction PES and reactions on the microscopic scale and provides students with the basic information they will need to understand what they see when they run a particular trajectory. However, students will require additional resources to fully understand the shape and topology of the three-dimensional PES. Many physical chemistry textbooks have a good three dimensional PES diagram, but even with this aid it is a good idea for the instructor to reinforce the physical topology of a reaction PES, perhaps using a threedimensional model (2). A set of exercises for students to perform and the associated questions to answer are also included. The questions encourage students to develop the connection between microscopic and macroscopic reaction kinetics. PTRJ conveniently fills a niche between the two programs Molecular Dynamics of the F + H2 Chemical Reaction (3) and Reaction Dynamics (4), published previously
by JCE Software. Molecular Dynamics provides an excellent introduction to all features of a PES and can be used to complement PTRJ’s introduction. Reaction Dynamics allows users to perform many different reaction trajectory calculations for a number of different systems. The many variables present in Reaction Dynamics may prevent a student from focusing on the nature of a single microscopic reaction on a PES. PTRJ focuses on one system with the pedagogical goal of understanding the relationship between the PES and the results of a particular trajectory. Once this connection has been made, Reaction Dynamics will provide students with a larger set of options with which to further explore microscopic reaction trajectories. Acknowledgments Stephen Prager, Paul Hladky, Daniel Firth, Jeff Benson, Bruce Prezzavento, Kenneth Leopold, and many others at the University of Minnesota made contributions to earlier versions of this program and provided helpful advice. Support for this project was received from both the University of Minnesota Chemistry Department and Rider University. Literature Cited 1. Porter, R. N.; Karplus, M. J. Phys. Chem. 1964, 40, 1105. 2. Dye, J. L. J. Chem. Educ. 1957, 34, 215. 3. Kutz, H. D.; Copeland, J. H.; Mathai, G. T. J. Chem. Educ. Software 1992, 4C2. 4. Lacks, D. J. Chem. Educ. Software 1992, 4C2.
Advanced Chemistry Collection
Simulation of the Physical Chemistry of Gas Chromatography John Haigh and J. R. Lord School of Science and Mathematics, Sheffield Hallam University, Sheffield S1 1WB, UK
Simulation of the Physical Chemistry of Gas Chromatography, for Windows-compatible computers, was developed as part of a physical chemistry unit on phase equilibrium. It uses moving frames, theory text blocks, and a simulation of equipment. Its aim is to show how basic principles, based on Henry’s law and the plate model, explain many of the features of gas chromatography. A physical chemistry unit designed to serve an applied chemistry course must provide a simulation that works according to a specific physical model: the student should see how simple physical chemical principles lead to a good approximation of realistic behavior on the column. To implement this aim, rather than observing the emergence of the sample at the detector as a single event and measuring a single retention volume for each species, Simulation of the Physical Chemistry of Gas Chromatography allows the student to visualize the movement of a sample and the carrier gas front through the column and then to measure the position of peaks at successive times and column locations by means of a graduated scale. A series of retention volumes can be measured for each sample. The equation relating the saturation vapor pressure, p0, and the activity coefficient, g, to speed is given in the theory 1528
section, but students are only required to understand its import and not to be able to derive or even to memorize it. A menu allows navigation between the sections of Simulation of the Physical Chemistry of Gas Chromatography. Experiments can be stopped and restarted easily. Many definitions and other technical points are available as hypertext. The student is encouraged to look quickly through the whole package, then to carefully work through the text and experiments.
This screen from Simulation of the Physical Chemistry of Gas Chromatography shows a Henry’s law experiment in progress.
Journal of Chemical Education • Vol. 77 No. 11 November 2000 • JChemEd.chem.wisc.edu
