Animations and simulations

CalTech Chemistry Animation Project A variety of high-end computers have been used to produce an interesting series of inexpensively-priced videotapes on a number of topics, suitable for high school or college use. From Nathan Lewis' group at California Institute of Technology.

Calorimetry simulation - this Web-based program by Gary Bertrand simulates a drop calorimeter for determining the specific heat capacity or heat of fusion of a selected metal sample. The page contains operating instructions, background discussion, and suggested experiments at beginning and advanced levels.

Kinetic theory simulations - here are some Java applets which permit the user to set parameters

Kinetic theory page by Julio Gea-Banacloche (U. Ark.) also allows exploration of microscopic reversibility; a special Macintosh version is available.

This one by an unnamed author at Michigan State U Division of Math & Science Education has a nice slider-based user inferface.

Learning Chemistry through Java - This site, by Eric Walter, Andrew Rappe and Charlotte Zales, offers on-line simulations of various topics. A Maxwell-Boltzmann applet allows one to simulate a velocity distribution histogram as it developes for various numbers of molecules at different temperatures. Under development (as of Jan 2001) are applets for plotting atomic wave functions, surface chemistry, photochemical kinetics, and optimization of a biomolecule structure.

This BlackLight Power site offers some unusually vivid animations of lattice structures, atoms and molecules, and quantum mechanics.

Leeds Chemistry Lecture Demonstrations - this site at Leeds University in the U.K. illustrates 40 chemistry demonstrations and provides access to several photo galleries illustrating a wide variety of phenomena. There is also a collection of lecture demo animations.

Quicktime movies of various molecular processes for chemistry educators are available for free download from this Molecular Arts

{The Chemist's Art Gallery} (2002-2004) at the Finnish Center for High-performance Computing and Networking offered some high quality animation and visualization images of molecular dynamics and other processes, as well as an extensive collection of links to other sites. (The link takes you to the Feb 2004 archive of this site.)


Atoms and orbitals

The Orbitron: a gallery of orbitals - Mark Winter of Sheffield U. has compiled this very nice collection of images representing orbitals, animated plots of wave functions and orbitals, "dot-density" plots of electron density and plots of radial distribution functions.

Some unusually good animated visualizations of atomic and molecular orbitals can be found at this site by by Stefan Immel of the Technical University of Darmstadt.

ChemViz The ChemViz group at NCSA has 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.

Atom-in-a-box is a Macintosh shareware application that displays atomic orbitals in real-time.

Atomic orbitals CD-ROM This product of Knowledge by Design provides information on atomic orbitals and extensive visualizations of their shapes.



EIC Exhibition Gallery - Selected lecture demonstrations published in the Royal Chemistry Society's Education in Chemistry journal. Descriptions and instructions can be found in selected issues on the EIC site under "Exhibition Chemistry. See also this compendium.

Macroscopic systems

Critical State of carbon dioxide Illustration of critical opalescence and development of a meniscus. From a 1968 C&EN feature article by Jan and Anneke Sengers.

Foods under the microscope - this extensive fascinating site contains many photos and links to food microsctructure. Compiled by Miloslav Kalab. (≤ 2006; archive inaccessible)



Jmol is a free, open source molecule viewer for students, educators, and researchers in chemistry and biochemistry. It is cross-platform, running on Windows, Mac OS X, and Linux/Unix systems. It includes the jMolApplet that can be integrated into Web pages, the Jmol application, a standalone Java application that runs on the desktop, and the JmolViewer, a development tool kit that can be integrated into other Java application.

Chemistry Visualization Resources for Teachers - an extensive annotated list by Rosa Hemphill.

History of Visualization of Biological Macromolecules - an interesting page from the U. Mass Rasmol group.

Inorganic structure database This is a collection of experimental structures of small molecules and ions compiled by Scot Wherland of Washington State U. Requires the WebLab viewer.

Library of inorganic structures - over 1600 structures of inorganic molecules, polyhedra and bioinorganic compounds, accessed through an interactive periodic table. Also at this site, a gallery of visually interesting molecules.

The Molecular Expressions Photo Gallery - A nicely organized collection of photomicrographs from Florida State U.

Molecule of the month. "Another month, another molecule" from a university or commercial Web site. Some will require an auxiliary viewer program or a suitable browser plug-in. (4/98)

Molecular Database - This site lists many examples of all the major VSEPR arrangements. For each molecule, structural information (including internuclear distances) is provided.

Online Macromolecular Museum - this artistically-designed site requires the Chime plug-in.

MathMol - MathMole home page - an introductory starting point for those interested in molecular modeling. - includes a K-12 activities section, hypermedia textbooks, and Library of 3-d molecular structures - Scientific Visualization Center, New York University

Molecular Arts Corp. offers a number of downloadable QuickTime movies. One shows how H2O molecules rearrange themselves as ice melts and changes to vapor.

World of Molecules - this site shows representations of molecules arranged by where the fit into both the natural and artificial world: foods, biology, pesticides, solvents, fuels, color, and materials.


Molecular graphics

Molecular graphics refers to the art and science of building visual representations of molecules, often very complex ones, and often with the purpose of showing special features such as solvent-accessible surfaces and docking sites. See this Wikipedia page or this one for an introduction to the subject.

See the Software Section below for more on molecular graphics.

Musical "visualizations" of protein and DNA sequences

This site by M.A. Clark of Texas Wesleyan University is something "completely different"!

Learning Biochemisry with Deep View - a gallery of graphics exercises for introductory biochemistry by Gale Rhodes, U of Southern Maine. See also the same author's Molecular modeling for beginners.

The Scientific and Artistic Uses of Molecular Surfaces – an interesting gallery assembled by T.J. O'Donnell.

Molecular Rover Project develops interactive environments of atomic-scale systems that allow the student to explore forces, structures, and motions from a microscopic viewpoint. "If we could mount a video camera on an atom like what NASA did on a Mars rover, what would we see? This is the mission of the Molecular Rover... With the central idea that the user can participate in a simulation by playing the role of an atom or a chemical group, a lot of new things can be borrowed from the gaming industry".


Nano-scale images, STM, AFM

Exploring the Nanoworld - a very nice site from the U. Wisconsin-Madison with linkds to visual materials, teacher modules, and many other resources.

Materials Science Image Gallery contains sections related to catalysis, crystallization, polymers and colloids, solid state and surface chemistry, and nanotechnology.

STM Image Gallery An interesting selection of images obtained with a Scanning Tunneling Microscope from the IBM labs.

Software for drawing and visualizing structures

Chemical drawing programs comparison - a very detailed description of several commercial software packages, with illustrations and links.

See also this comparison of several popular chemical drawing programs.

Jmol is a free, open source program for viewing three-dimensional chemical structures. It is intended for students, educators, and researchers in chemistry and biochemistry. It is cross-platform, running on Windows, Mac OS X, and Linux/Unix systems. Features include reading a variety of file types and output from quantum chemistry programs, and animation of multi-frame files and computed normal modes from quantum programs. The Jmol Wiki provides many inormative links, including to other sites that use Jmol. See also this Jmol Examples page.

Rasmol is one of the first open-source visualization programs, intended mainly for the interactive depiction of complex biomolecules. Protein Explorer is a more developed and easier-to-use derivative of Rasmol. It is free, and runs on Windows or Macintosh/PPC computers. There are several Web-based tutorials on Rasmol; this RasMol Tutorial by Gale Rhodes of U. of S. Maine might be a good place to start.

JChemPaint is a similar open-source, cross-platform, free software editor for creating molecular structures in two dimensions.

The Chime Plug-in is free software that enables your Web browser to display and manipulate molecular structures. Liz Dorland's {Beginner's Guide to Chime} (link is to archived last update 2004) is a good place to start; for a more extensive collection of Chime-related links (including links to actual structures), see the Chime Resources Page by Eric Marz, U. Mass - Amherst.

The Molecular Literacy Project (a Concord MA consortium) is working to enhance science and technology teaching in grades 10-14 by providing Molecular Literacy content in support of careers in biotechnology and nanotechnology. Two components of the Concord, MA Molecular Literacy Project project, Molecular Logic and Molecular Workbench, offer free open-source software along with teachers' materials.

A set of curricular material built around the use of the Spartan molecular modeling software and aimed at the high-school level can be found at the excellent site put up by Mike Ellison and Rosa Hemphill.

Astonis Virtual Studio (Avisto) - a set of Windows-only Java-based applications scientific computing tools with structure-drawing and molecular modeling software. The site links to a list of educational applications.

Symyx Draw is a free-for-noncommercial-use Windows-only application from ACD that you can use it to draw chemical structures and export them for viewing as 3D models. Symyx Draw is a successor to Isis/Draw which is no longer available.

> ACD/ChemSketch is a free-for-noncommercial-use application for Windows or Linux that offers 3D optimization, viewing and rotation, cut and paste into other applications, and tautomer prediction.

ChemDraw "is the industry standard software used by scientists worldwide to draw accurate, chemically-aware structures for use in database queries, preparation of publication-quality graphics, and entry for modeling and other programs that require an electronic description of molecules and reactions." Versions are available for both Windows and Mac-OS, and a deep discount is available to academic users.

CompuChem offers MolView, a drawing program that produces ray-traced 3-d molecular models, and Chem Tools which features a large collection of glassware parts images for constructing apparatus diagrams.

Crystal Designer This Macintosh application allows one to build crystal structure diagrams. A free Demo version is available.

> eChem is a free simplified and learner-centered design version of professional visualizing tools. It allows students to build and manipulate three-dimensional models of molecules with a visualizer module. It also allows students to compare computationally predicted properties of the molecule with properties they observe in the laboratory. Note added 2/2006: this software is no longer in development and does not run under Mac OS X.

iMol is a free molecular visualization application for Mac OS X operating system. iMol supports several file formats. It can easily handle small and large molecules, loads multiple molecules, can move and rotate them independently, or displays a molecular dynamics trajectory.

MDL Information Systems provides downloads of Chime and Isis-Draw (Mac/Windows) from their site.

MoluCAD is a full-featured molecular modeling and visualization tool designed for personal computing platforms. It was developed with NSF support and is available to students at a very low price. Both Macintosh and Windows formats can be downloaded in demo, "lite", and multiple-pack versions for class use.. The latest version incorporates many advanced features only found in expensive workstation-based modeling packages. Novice users are able to quickly generate models, view them form any perspective, create reaction animations, and save all data to disk. 

Drawing chemical structures with PLT for Windows - free shareware; see this link for examples.

EasyChem - a program designed to draw chemical molecules, written under Linux and using Gtk+ 2. A MacOS X build is available.

Stark Design's Atomic Microscope software package allows you to model large collections of molecules.

RasMol Home Page - RasMol is free software for looking at molecular structures. It runs on Windows or Macintosh/PPC computers (also Unix).

VRML (Virtual Reality Modeling Language is a scheme for representing three-dimensional objects (molecules) on a display screen. Molecular modeling with VRML; VRML in Chemistry article.

U Rhode Island home page - This home page of URI's Chemistry Department and other pages at this site contain some nice molecular images and movies.



Visions of Science - Photographic awards sponsored by Novartis and The Daily Telegraph