Chemistry Visualization Links

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Here's a collection of multimedia chemistry resources on the Web. Some items are dated, so please notify me if you find dead links or find new items.
The colored symbols at the end of each link indicate the document type (for details, go to the glossary). To submit an entry or report a dead link, drop me a line at

Glossary | Nucleic acids chemistry | Protein chemistry | General | Organic
| Physical/Theoretical | Games | Software | WWW

Nucleic acids chemistry:


PDB Search/view structures in the Protein Databank. (WWW, Jmol).

KEGG: Kyoto Encyclopedia of Genes and Genomes (WWW).

Nucleic Acids Database (WWW).

Specific Topics:

Cisplatin: anti-cancer drug (Quicktime).

E. coli Genome Center (WWW).

E. coli Genome Report (WWW).

The Genome Navigator (Java).


Protein chemistry:


PDB Browser Search/view structures in the Brookhaven Protein Databank (RasMol).

ExPASy (SWISS-PROT: Annotated protein sequence database) (WWW).

Specific Topics:

foldit amazing protein folding game (Win, Mac, Linux)

A Complete Course on the Principles of Protein Structure (WWW).

Protein Architecture uses Protein G as an example to illustrate protein architecture (Chime).

Protein structure tutorial A RasMol-based tour of the structural features of globular proteins (RasMol).

SCOP: Structural Classification of Proteins (WWW).


General Chemistry:


Organic Chemistry "Flashware" 130+ animations: Lewis structures, arrow-pushing, mechanisms, LCAO interactions (Flash).

Chemistry WebBook (WWW). (WWW).

irYdium Project (WWW).

Virtual Chemistry Lab (irYdium Project) (Java)

Virtual Chemistry Laboratory (Oxford U.) (WWW)

Periodic Tables:

Web-Elements: The online periodic table database (WWW).

Periodic Table (irYdium Project) (Java)

Specific Topics:

Atmospheric Fixation of Nitrogen (Quicktime).

Dynamite Chemistry (Quicktime).

Equilibrium (irYdium Project) (Java)

Orbitals (Shockwave).

Representing Compounds (Shockwave).

Stoichiometry (irYdium Project) (Java)

Structure and Chemistry of Coordination Compounds (Chime).

VSEPR, Coordination compounds (Purdue University) (WWW).

What is a Dihedral Angle (Shockwave).


Inorganic/Organometallic Chemistry

LiveChem (Virtual Chemistry Laboratory, Oxford U.) (WWW)

Hydrogenation of Alkenes with Wilkinson's Catalyst (Quicktime).

Hydrogenation of Alkenes with Wilkinson's Catalyst (Shockwave).

Inorganic Reaction Mechanisms 1 (WWW).

Introduction to NonMetal Chemistry (WWW).

Mechanisms of Organometallic Transformations (WWW).

Metal Ions in Solution (Virtual Chemistry Laboratory, Oxford U.) (WWW)

Organometallic CO Insertion by Methyl Migration (Shockwave).

Organometallic Synthesis (Virtual Chemistry Laboratory, Oxford U.) (WWW)

Structure of Solids (WWW).

Structure and Chemistry of Coordination Compounds (Chime).

Symmetry (Virtual Chemistry Laboratory, Oxford U.) (WWW)

VSEPR (Virtual Chemistry Laboratory, Oxford U.) (WWW)


Organic chemistry:


Organic Chemistry "Flashware" 130+ animations: Lewis structures, arrow-pushing, mechanisms, LCAO interactions (Flash). (WWW).

Global Instructional Chemistry (WWW).

Intercollegiate Organic Chemistry (WWW).

Organic Chemistry Molecules and Tutorials (Chime).

Combinatorial Chemistry Review (WWW).

Physical Properties of Alkenes (Shockwave).

Protecting Groups ( (WWW).

Functional Groups:

Aldehydes and Ketones (Shockwave).

Amines (Shockwave).

Enolates (Shockwave).

Alpha,Beta-Unsaturated Carbonyls (Shockwave).

Reaction Mechanisms:

Organic Chemistry "Flashware" 130+ animations: Lewis structures, arrow-pushing, mechanisms, LCAO interactions (Flash).

Interactive Organic Mechanisms (Virtual Chemistry Laboratory, Oxford U.) (WWW)

Named Reactions ( (WWW).

Named Organic Reactions (Virtual Chemistry Laboratory, Oxford U.) (WWW)

Carbocationic Rearrangements (WWW).

Electrophilic Aromatic Substitution (Shockwave).

Pericyclic Reaction Mechanisms (Tutorial Problems) (WWW).

Pinacol Rearrangment (Shockwave).

Reaction Drill Flashcards (WWW).

SN1 vs SN2 (Shockwave).



The Spectral Game: great online game for NMR drills (WWW).


Specific Topics:

Alkane Physical Properties (Shockwave).

Asymmetric Synthesis: A Didactic Survey, by Carmen Lopez-Leonardo (Spanish) (WWW).

Brevetoxin B (Quicktime).

Chirality, Stereoisomers, Optical Activity (Shockwave).

Computational Chemistry (Shockwave).

Conformational Analysis Tutorial (WWW).

Dihedral Angle (Shockwave).

Mass Spectrometry (Shockwave).

Representing Compounds (Shockwave).

Stereochemistry (Shockwave).

Stereochemistry Online Page: Great tutorial on stereoisomers, has many exercises in multimedia format (Chime).

Taxol (Quicktime).


Organic Laboratory:

Laboratory techniques videos: Great videos from U. of Alberta (Quicktime, WMV).



Physical/Theoretical Chemistry

Analysing 2D NMR Spectra using Hyperactive Molecules (RasMol).

Arrays in NMR (WWW).

Basic Manual Operation of the Unity 300, 400 and 500 spectrometers (Acrobat).

Calibrations, decoupling, T1,Kinetics, NOE, Using Arrays (WWW).

Computational Chemistry (Shockwave).

Computational Chemistry Teaching Modules (WWW).

COSY Experiments (WWW).

FTNMR FID Archive (NUTS Format) (WWW).

MathMol Library of 3-D Molecular Structures (VRML).

Molecular Structure Calculations (Shockwave).

NMR: A Short Course (WWW).

NMR Data at Widener University (WWW).

Notes About FT and Digital Resolution in NMR Experiments (WWW).

NMR Experiments Using s2pul (vnmr) (WWW).

Particle in a box (irYdium Project) (Java)

Practical Excercises in Quantum Chemistry (WWW).

Spectroscopic Simulator (irYdium Project) (Java).

Statistical Mechanics Simulator (irYdium Project) (Java).

Undergraduate NMR Lab Exercises (WWW).




Computer games:

foldit - protein folding game (Win, Mac)

ChemTiles - organic chemistry (WWW)

Spectral Game - NMR problems (WWW)

Jeopardy! Organic Chemistry Game - organic chemistry game (WWW)

Rags to Riches - organic chemistry quiz (WWW)

Other games:

Wheel of Orgo - organic synthesis game using tablet PC (Win)

Organic Chemistry Game - organic chemistry card game





Molecular viewers:









Other WWW Chemistry Resources

UCA's Chemistry Links (WWW).

ChemFinder WebServer Project (WWW).

Chemistry Pointers (Knut Irgum) (WWW).

Internet Resources for Science and Mathematics Education:Chemistry

Yahoo Search: Chemistry

Glossary of multimedia types:

  • Acrobat: Adobe Acrobat portable document format (.pdf). Requires the Adobe Acrobat Reader.
  • Chime: Interactive 3D structures manipulation. Requires the free Chemscape Chime plug-in.
  • Flash: Interactive animations. Requires Macromedia Flash plugin/player.
  • Java: Java applets. Requires a Java-ready browser (i.e. Netscape, Internet Explore).
  • Jmol: Interactive 3D structures manipulation. Requires Java-enabled browser.
  • Kinemage: Contains 3-D structures in Kinemage format. Requires the free Mage software.
  • Mac: Mac application.
  • Linux: Linux application.
  • MPEG: MPEG movie clips. Requires an MPEG player (i.e. Sparkle (Mac)).
  • Quicktime: Quicktime movie clips. Requires Quicktime viewer or plug-in.
  • QTVR: Quicktime VR models. Requires Quicktime player , Netscape and QTVR Components.
  • RasMol: Interactive 3D structures manipulation. Requires RasMol program.
  • Shockwave: Interactive animations. Requires the free Shockwave plug-in.
  • VRML: VRML 3-D environments. Requires Netscape and the Live3D plug-in.
  • Win: Windows application.
  • WMV: Windows Movie file. Requires Windows Media Player or other player.
  • WWW: Simple WWW documents. Best viewed with Netscape or Internet Explorer.


updated November 23, 2010

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