Chemistry Teaching Resources
Graphics and Visualizations
- 3D molecular structures
A collection of 3D molecular structures of benzotriazoles and some solvents for visualization with ChemScape Chime.
- Amazing Science at the Roxy®
This is a place where you can look at and download physical science activities. There are activities that are aimed towards the student and are available in the areas labelled Demomania,National Chemistry Week WonderScience and The Observatory. These may include movies and sounds, but are designed to be interactive.
- Amino Acid Database
Includes a 3-D image of each amino acid in the DB.
- Animated Infra-Red Spectroscopy (AIRS)
This website contains animated infra-red spectra for a variety of organic compounds. Each spectrum allows access to animated molecular vibrations for many of its peaks. Clicking on a particular peak will download the animation of the corresponding vibration. From Michigan State University.
- All About Atoms
All About Atoms is a very basic overview of atomic structure. Students can click on particles to learn more about them and even discover some fun facts about atoms!
- Animated GIF's and Protein Chemistry
The utility of animated GIF's goes far beyond the ability to rotate your companies logo or having bouncing buttons or whatever ridiculous things are being created these days. This page demonstrates the concept by multiple views of Carboxypeptidase A with peptide substrate rotating on an axis. This way one can get a feel for the 3-D structure of the enzyme with its substrate bound in the active site, as well as the position of some key side groups.
- Atomic Theory
A clickable periodic table serves JPEG images of hydrogenic wave functions. 3D Models of Atomic Orbitals are presented in VRML/Webspace format.
This manufacturers of space-filling molecular modeling kits carries a tutorial section on molecular modeling, pictures of various molecular models, and some links.
- Banque de molécules et d'ions ne contenant pas d'éléments de transition
About fifty files with the .pdb format to describe the geometric characteristics of simple inorganic molecules. These files were made with the atom's coordinates to respect the experimental values. So, these files permit the illustration of classical geometries learnt in the VSEPR method.
- Biochemistry Graphics
A collection of animated and still graphics which illustrates significant biochemical concepts and processes.
- Biological Sciences 102 - Molecules and Stuctures Homepage at U. C. Davis
A link list to 3D structure pages and sites such as Amino Acid Properties and sites with other biological molecules.
- Brookhaven Protein Data Bank
PDB, the single international repository for the processing and distribution of 3-D macromolecular structure data primarily determined experimentally by X-ray crystallography and NMR.
- C4-Computers in Chemistry at Cabrillo College
A library with more than 400 "live" molecules, including almost all commonly studied compounds. Sets of chemistry problems incorporating Chime models. Most features of this site require Netscape Navigator 3.01 or later and the Chime plug-in. Cabrillo College Chemistry Department also offers a Chime Tutorial.
The ChemVis project is one of 23 research projects in the strategic research initiative "V3D2" ("Distributed Processing and Exchange of Digital Documents") of the German Research Foundation (Deutsche Forschungsgemeinschaft DFG). The group develops new tools for chemical visualization within the internet. Some project demos are available (require a VRML97 plug-in). A German version of the site i also available.
- Chemistry at Imperial College of Science, Technology and Medicine
The 3D Virtual Chemistry Library Project. Includes a Molecule Library.
Exercises in Molecular Symmetry. Hands on exercises with simulations of molecular motions in different symmetries.
Web compatability table for Chemists. A table of chemically applied web browser tests.
The Chemical MIME Home Page. This page provides a concise entry point for various information sources relating to chemical MIME (Multipurpose Internet Mail Extension).
- Chemistry Animated Reaction Mechanisms
ChARMs is an interactive multimedia CD for teaching and learning organic chemistry. It contains >800 screens of Lectures and ~250,000 frames of animations and is designed for use by both Academics and Students.
- Chemistry Art Gallery
This site in Finland contains spectacular visualization and animations in chemistry done at the Visualization and Animation Laboratory at CSC.
- Chemistry Comes Alive!
Movies and animations with close-ups of reactions, physical changes, and techniques, all listed by topic. The material is also available on a CDROM where the movies and images are all larger and of higher quality. Produced by the Division of Chemical Education, ACS.
The ChemViz group at NCSA has, within an NSF sponsored program, developed material which can put high-powered computing and communications tools into the hands of high school teachers and their students. These materials allow high schoolers and their teachers to do their own research by visualizing atomic and molecular orbitals using computational methods. There is also an FTP site associated with the ChemViz project.
- Chemistry Clip Art
Simple black-and-white (1 bit) freeware chemistry-related clip art. Organized in a HyperCard stack or MacPaint files.
The Chemland program set is designed to be used by chemists and chemistry students for the study of the principles of chemistry. The program set has been created with the philosophy that students should learn chemistry by exploring how chemical substances behave in nature. Concepts are visualized with Java applets that use the Java Plug-in. There is also a non-plug-in version for each applet.
- Clipart of Common Laboratory Glassware
Clipware is a collection of clipart of common laboratory glassware, provided to you at no charge by CambridgeSoft Corporation and Ace Glass Incorporated. You must own a copy of CS ChemDraw version 3.0 or later to use this clipart, which is provided as a ChemDraw Template document for ease of use. All glassware is in EPS format for the highest output resolution. Also, all glassware shares the same standard joint sizes, so that different pieces may be combined to form complicated arrangements.
- Common Glassware
Picture gallery of glassware found in chemistry laboratories. (Copyrighted material from Chemistry Clipart by Molecular Arts Corporation, Anaheim, CA)
- Creating Enhanced Web Pages for Chemistry
A tutorial for enhancing your web-site with visualizations of molecules and other material. The site also includes a link list with downloadable software useful to the editor of a chemical web page.
- Crystal Lattice Structures
A systematic presentation of crystal lattice structures. Coordinates in .xyz-format may be downloaded or visualized with the ChemScape Chime plug-in.
- Crystal Structural Models using Chime Plug-in
Structures of mineral groups with descriptions.
- Diels-Alder Reactions
The simulations were constructed as part of an Undergraduate thesis in Applied Chemistry. Viewing the animations require the Chime plug-in, QuickTime or a MPEG player. By Barry McCarthy, 1996, Brunel University.
- Educational Applets
Chemical animations with Java applets at the University of California at Irvine (UIC). In order to use any applet you must have a browser that supports Java applets. Netscape Navigator 2.0+ and the Sun HotJava browser support applets.
- Examples of complexes derived from common ligands
3D structures of ligads with formula an IUPAC name. Ths structures can be viewed with RasMol or the ChemScape Chime plug-in. From University of the West Indies, Mona Campus.
- The Fullerene Gallery
The Fullerene Gallery contains a library of Fullerene structures which can be viewed interactively, provided your browser is Java enabled, or downloaded as Cartesian coordinates.
- Hetero-compound Information Centre (HIC-Up)
The Hetero-compound Information Centre - Uppsala, a freely-accessible resource for structural biologists dealing with hetero-compounds ("small molecules"). The database can be searched by compound name, formula etc. This service is provided and maintained by Gerard J Kleywegt at the Department of Cell and Molecular Biology, Uppsala University.
- Hyperactive Molecules
This is a collection of molecules from servers around the world which can be viewed interactively. Turn off in-lined images before going to the site in England to minimize transfer time. If you want to view a molecule just click on the placeholder icon.
- IMB Jena Image Library of Biological Macromolecules
The library contains visual and other information on three-dimensional biopolymer structures. It provides access to all structure entries deposited at the Protein Data Bank (PDB) or at the Nucleic Acid Database (NDB). In addition, general information on the architecture of biopolymer structures is available. The major part of entries has automatically generated images and interfaces for free molecular graphics programs. However, the number of manually generated high-quality and informative mono, stereo and VRML representions is steadily increased and remains one of the peculiarities of the IMB Jena Image Library.
- Indiana University Molecular Structure Center
The IUMSC site makes extensive use of Java applets to allow users to generate molecular graphics for structures determined by X-ray crystallography. Over 200 molecules have been added so far, with several thousand to eventually be added fro the IUMSC archives. "Common Molecules" page is worth looking at also, as is the "crystallography and morphology" pages.
- The Internet as a Chemistry Tool
Resources relating to Internet as a chemistry tool. Links compiled by Henry Rzepa.
- Java 3D molecular viewer
A molecular viewer in Java used to browse a metalloprotein database. The browser has some special features, such as showing distances and angles between selected atoms. More info is found at the MDB Main Page.
- J. Lauher's Fullerene Structure Library
Images of various Fullerene structures.
- Molecular Models
Molecular models kits and other educational lab equipment sold by Indigo Instruments.
- MathMol - Mathematics and Molecules
The main objective of MathMol is to provide students, teachers, researchers and the general public with information about the rapidly growing fields of molecular modeling and related areas.
- MicroScapes - The Gallery
This page contains a number of electron micrographs of crystals, surfaces, etc. The MicroScapes images are created in collaboration with the scientists and researchers of Lucent Bell Laboratories.
UCSF MidasPlus is an advanced molecular modeling system developed by the Computer Graphics Laboratory (CGL) at the University of California, San Francisco. The software is distributed as documented source code to serve as both a starting point and training tool for others interested in doing their own software development. There is also an image gallery available at the same site.
- Models of Small Molecules in .pdb Format
Databases with molecules in a format for visualizing with RasMol or the ChemScape Chime plug-in.
Okanagan University College: Hundreds of small organic molecules.
Webmolecules: Over 200,000 molecular models online sorted by category, formula, fragments, valences or orbitals. Search by formula, CAS number, NSC number or common name. Viewing molecules require VRML or ChemScape Chime.
MathMol Molecular Library: Contains water, carbons, hydrocarbons, molecules of life and drugs.
Smell Database: Structures and properties of smelling molecules.
Molecular Virtual Reality: Complexed crown ethers. Molecules also in .wrl format.
ALB Crystallography: 6-Connected 3D Nets.
Okanagan University College: An Introduction to Basic Organic Nomenclature.
Pomona University: Structures of Molecules Discussed in Class (Chemistry 1).
Widener University: Visualizing Molecules. This page contains a set of Lewis Dot structures, Hyperchem 3D renderings, and Protein Databank files (*.pdb) for a variety of molecules. These were developed for teaching molecular structure in General Chemistry at Widener University.
University of the West Indies, Mona Campus: Jamaican themes for Lecture Material: "The extraction of alumina from bauxite", "The Chemistry of spices", "Jamaican Blue Mountain coffee", "What is at the fruit and vegetable market?", "Jamaican Rum from sugar cane", "Synfuel from Ethanol", "Marine Natural Products", "Herbal remedies". PDB molecules are found in context in the lecture material.
The Three-Dimensional Drug Structure Databank: The Three-dimensional Drug Structure Databank consists of a collection of investigational and approved therapeutic agents whose structures have been experimentally determined or built using molecular modeling methods.
Molecules of the Month: Links to MOTM Oxford, MOTM Bristol, and MOTM University of Erlangen-Nuernberg. Each month a new molecule will be added to the list on this page. The links will take you to a page at one of the Web sites at a University Chemistry Department or commercial site in the UK, the US, or anywhere in the world, where useful (and hopefully entertaining!), information can be found about a particularly interesting molecule.
Die Organik-Galerie: A selection of organic molecule images obtained by raytracing as well as .pdb and .wrl downloadable structure formats.
WWU Virtual Molecular Model Kit: A variety of instructional organic molecules.
- Molecular Animations with Re View
A variety of molecular animations/simulations are available at this site, covering conformational analyses, reactions, vibrations, etc. Both animations and multistructure XYZ files are provided, enabling movies or '4D'-simulations to be viewed. The latter will require a special player such as ReView [demo] or XMol .
- Molecular Animations of Large Molecules
AVI movies of large, biological molecules (hemoglobins, agarose, DNA, collagen and more).
- Molecular Dynamics Simulations on Large Systems
The objective of this project is to perform molecular dynamics simulations on extremely large systems, consisting of up to 106 atoms, and to analyze the results in real time.
- Molecular Models for Biochemistry at CMU
The linked pages described here have tutorials and quizzes that are based on Chime and RasMol images of the molecules and macromolecules found in biochemistry. They are intended to complement standard biochemistry texts where more explanation is provided, but where interactive 3-D images of the molecules are not available.
- Molecular Movies
Nine interactive animations describing nucleophilic substitutions, eliminations, electrophilic additions, electrophilic aromatic substitution, nucleophilic addition, and nucleophilic substitution on acid derivatives. Three demo files are playable in a web browser, if the Shockwave plug-in is installed.
- Molecule of the Month
Each month a new molecule will be added to the list on this page. The links will take you to a page at one of the Web sites at a University Chemistry Department or commercial site in the UK, the US, or anywhere in the world, where useful (and hopefully entertaining!), information can be found about a particularly interesting molecule.
- Molecules in 3D
A few examples of molecules to be viewed in 3D. A 3D effect requires red-blue glasses.
A hypertext-based table of contents of the Brookhaven Protein Databank. Allows on-the-fly generation of 3D-images in various formats from the enormous database.
MolPOV is a graphics file converter that reads Brookhaven Protein Data Bank formated files and produces a ready-to-render input file for the Persistence of Vision (POV) ray tracer. The PDB files can be from the Brookhaven PDB itself or from any molecular modeling program that can store structures in the PDB format. Both programs are freeware.
Images from the Center for Microscopy and Microanalysis, University of Queensland, Australia, an interdisciplinary research and service facility dedicated to an understanding of the structure and composition of all materials at atomic, molecular, cellular and macromolecular scales.
- NCSA Digital Information System - Chemistry
Visualizations of various chemical reactions and phenomena.
- NIH Guide to Molecular Modeling
The NIH Guide to Molecular Modeling is being developed by members of the Computational Molecular Biology Section (CMB) of NIH's Division of Computer Research and Technology (DCRT). This project is part of an overall effort to help educate NIH researchers and others in the theory and practice of molecular modeling.
- NIH Molecular Modeling Home Page
Intended as a centralized source of information concerning the methods and biological applications of molecular modeling.
- Normal Modes of trans-1,2-Dichloroethylene
- Nucleic Acid Database
The Nucleic Acid Database Project (NDB) assembles and distributes structural information about nucleic acids.
- Orbital Viewer
Lots of atomic orbitals, arranged by quantum number and shape. The orbitals images are produced with the Orbital Viewer, an amazing software for drawing and viewing orbitals in 3D, which may be downloaded for free from this site.
- Persistence of Vision Raytracer
The Persistence of Vision Raytracer is a high-quality, totally free tool for creating stunning three-dimensional graphics. It is available in official versions for Microsoft Windows 3.1/Win32s and Windows 95/NT, DOS, the Macintosh, i86 Linux, SunOS, and Amiga. The source code is available for those wanting to do their own ports.
- Protein Science Kinemages
A 'kinemage' [kinetic image] is a scientific illustration presented as an interactive computer display. Operations on the displayed kinemage respond within a fraction of a second: the entire image can be rotated in real time, parts of the display can be turned on or off, any point can be identified by picking it, and the change between different forms can be aninmated. Kinemages are proposed as a subtype of the chemical MIME standard with the specification "chemical/x-kinemage" and file extension "kin". Kinemages, their history, and the proposed MIME standard are described in mime_kin.txt in the MIME_kin directory of the Protein Science gopher server.
- RasMol Home Page
RasMol is free molecular visualization software, great for small molecules but is especially amazing for macromolecules (proteins, DNA, RNA) or macromolecular assemblies (viruses, lipid bilayers). This site provides the software itself, a gallery of images produced by RasMol, educational scripts (movies) for projection in lectures or for self-study, links to class web sites which employ RasMol, and to other free molecular visualization software.
- Representation of Molecular Models Rendering Techniques
This is a nice tutorial on the ways that molecules can be represented by computer imaging. Includes discussion on structures, surfaces, rendering, etc.
- Scanning Tunneling Microscopy
An STM image gallery and more from The Visualization lab of IBM.
- Senses Bureau - The Wilson Group
Contains visualisations related to teaching of general and physical chemistry at the University of California at San Diego.
- Silicon Graphics Teaching Laboratory
Contains a course on molecular modelling and information on MacroModel.
- SMILES Tutorial
SMILES is a simple yet comprehensive chemical nomenclature. The answer to the most commonly asked question about SMILES is: yes, it is an acronym, meaning Simplified Molecular Input Line Entry Specification. SMILES is widely used as a general-purpose chemical nomenclature and data exchange format. This document is intended to serve as a comprehensive tutorial for the SMILES language itself.
- TORVS Chemical Internet Services
Contains searchable databases with 3D coordinates, GIFS, and VMRL scenes for Chemical Structures as well as chemical database browsers.
- UK Chemistry Database Service
The primary aim of the service is to help chemists solve their problems. This is done by providing chemical databases, help, training and information - free of charge to all UK "academics".
- UK SuperJanet Demonstrations
QuickTime movies, playable on either Mac or MS Windows using appropriate software.
- University of Arizona QuickTime Movies
Annotated QuickTime movies organized by lecture topic:
Molecular Recognition (DNA)
Effect of Oxygen Binding on Heme
SN2 Reaction Mechanism
PDB files can be viewed interactively with the Chime plug-in or RasMol.
- Videos for Chemistry
The School of Chemistry, Leeds University has a number of video demonstrations that are uses to supplement their own teaching and which can be supply at reasonable cost (roughly USD 45.00 per hour of video including teacher notes) to other educational establishments.
- Virtual Chemistry Lab at the University of Oxford
A virtual reality chemistry lab that includes a three dimensional simulation of the University of Oxford's inorganic chemistry teaching lab and interactive on-line experiments. Examples of material available now or in the process of being built include a QuickTime3 VR tour of a laboratory, preparation of a superconductor (with videos of the special properties of such materials), and exploring the aqueous chemistry of common metal ions. This site makes extensive use of plug-ins and multimedia. You'll need Netscape Navigator 3.0 or Internet Explorer 3.0 to view it sucessfully. It's a good site to see what is possible with many emerging technologies including VRML, QuickTime, QuickTime VR, Real VR, and Macromedia Shockwave.
- Virtual Molecular Model Kit
- VRML in Chemistry
A new technique to provide chemistry related information is presented. The approach is based on the Virtual Reality Modeling Language (VRML) which extends the WWW interface with the additional ability to visualize 3D object oriented scenarios and interact with the basic elements.
- WebMolecules - An interactive 3D Library of Molecular Models
Over 200,000 molecular models are now on-line. Includes molecules of educational importance, commercial significance, and topical interest. Also orbitals, valences, and fragment models. Supports both Chime and VRML plug-ins. Indexed and searchable. Very cool.
- WebSpace Author
WebSpace Author is a sophisticated, yet easy-to-use application that provides all the tools needed to add compelling, high-performing 3D content to a Web site. Silicon Graphis offer evaluation versions of their software as well as free software.
- The WWW Chemical Structures Database
Claims to be the first non-textual search engine operating on data found in Webspace. The WWW chemical structures database contains more than 2250 automatically collected chemical structures from the Internet, complete with information about the refering HTML pages. This database is searchable with the usual chemical search operations - full-structure and substructure search, formula search, name search, and more.
Welcome visitor since 1996-03-08.
Last modified Thu Feb 08 14:45:42 2001 by firstname.lastname@example.org - Data is 50565 bytes
Knut Irgum, Analytical Chemistry, Umeå University, S-901 87 Umeå, Sweden.
© Copyright, Knut Irgum, 1995-2001. All rights reserved.