Links: Applets and Visualizations
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Applets and Visualizations
Read this information before installing the Chime plug-in and save a lot of time. Also describes how to place interactive molecules on a webpage.
MDL's free Chime plug-in makes possible the presentation of 2-D and 3-D molecules directly within a web page. The molecules in the web page are "live," meaning they are not just still pictures, but chemical structures that can be rotated, reformatted, and saved in various file formats for use in modeling or database software.
3-D molecular visualization freeware.
Intuitive chemical drawing program that supports all the normal features plus Markush bonds, aromaticity, and tautomers. Clean and optimize a structure, and view in 3D with a click. Freeware version available for download.
Animated ball-and-stick animations of amino acid basics: structure, peptides, tertiary structures. Require Macromedia's Flash Shockwave plugin.
Contains "hyperactive molecules", three-dimensional structures that students can rotate and manipulate similarly to molecular model kits conventionally used in the laboratory. In addition digital photos provide step-by-step instructions on how to assemble molecular structures.
An introduction to the basics of molecular modeling. The text treatment is an asset to understanding the concept. Do not be distracted by the accompanying equations.
Lists of sites for free viewer and plug-in software, visualization Demonstration sites, GIF depictions...
A quick tour of the reasons why molecular modeling is becoming so important to chemists...from drug design to creation of new materials.
An good site for learning how to predict the three-dimensional structure of molecules. Requires the chime plug-in to view and manipulate the images presented in this tutorial. Useful because it approaches chemical structure in different ways such as: Lewis structures, formal charge, resonance structures, VSEPR theory, bond and molecular polarity, and intermolecular forces.
Nice introduction to naming and drawing alkanes, cycloalkanes, alkanes with chiral centers, alkyl halides, alkenes and alkynes, alcohols and ethers, and carbohydrates. The ability to rotate the exercise molecules in 3-D without a plug-in is a very attractive feature.
Libraries of 3-D Molecules
3-D structures for water/ice, carbon, hydrocarbons, amino acids, drugs... Click on GIF to enlarge image.
3-D views of about 20 compounds including CH4,O3, H2O, SO2, CH3CH2OH... Requires RasMol.
A library of 150 molecules that you can display and manipulate in three dimensions using MDL's Chime plugin. The molecules are sorted into six sections. 'Simple molecules' includes gases, alcohols, acids, fuels, fats, and soaps.
A comprehensive listing of 3-D pharmaceutical structures which can be viewed, rotated, and animated live on your screen with Chime, the Chemscape plug-in by MDL. 3-D animated structures demonstrate how molecules actually move and rotate on their bond axis.
An examination of properties and structure of amino acids. Requires Chime plug-in for visualization and rotation of the amino acids in 3-D. Molecular structure and pKa's available without Chime plug-in.
A collection of structures of coordination compounds, crystal stuctures, binary inorganic compounds and organic moles such as hormones, morphine analogs and neurotransmitters which can be viewed with or without Chime plug-in. Use the Chime plug-in for rotation of the molecules.
A large collection of 3-D molecular structures. Requires the Chemscape Chime plugin. The list of structures includes: amino acids, nucleic acids, polymers, plus drugs such as aspirin, caffeine, cocaine, LSD, morphine, nicotine, penicillin…
Two structural representations The top structure shows all the bonds and atoms in the hemoglobin molecule. The bottom structure is a more common representation with carbons represented by the junction of two bonds, hydrogens and heteroatoms shown explicitly.
Discussion of the structure of simple inorganic solids and a practice sequence intended to help understand the manner in which the regular structures of some simple inorganic solids are constructed. Chime is required for rotation.
A site for the display and study of macromolecules. The Chime plug-in is required. There are interactive tutorials on individual molecules in which hypertextual explanations of important biochemical features are linked to 3-D image of the molecule of interest.
Good still graphics illustrating ball-and-stick, wire frame, and space filled models of the inorganic molecule ferrocene. Click on image to enlarge.
Over 400 molecules available for viewing. Requires Chime plug in.
An eclectic group of molecules presented in an eclectic format. Some of the molecules do not include a structure visual while others have structure presentations that can be enhanced by the Chime plug-in. A site worth investigating. Series includes Water, Ozone, Urea, Sulfanilamide, Vitamin B12, C60 Buckyballs, Diamond, Digitalis, Aspirin... Click on MOTM Bristol and scroll down to the molecule of choice.
Very well done, unusually clear, 3-D visualizations of amino acids, nuclei acids, proteins.. Requires Chime and worth the effort.
A library of 3-D structures that includes ferrocene, amino acids, DDT, cholesterol, Viagra, water, Ecstasy, Valium, Prozac, urea, phenol, formaldehyde, quinine, buckeytubes. Click on MOTM Oxford and then on red "text only" at bottom of page. Requires Chime plug-in for rotation control.
This brief tutorial covers the chemical and structural properties of the 20 Amino Acids commonly found in proteins. Images are given but can also rotate amino acids using RasMol.
3-D presentation of the structure of elements, halides, oxides, C60 fullerene... Requires Chime for full effect of 3-D rotation.
Illustrates some of the basic points of conformational analysis using open-chain molecules, cyclohexane systems, and hetreocyclic systems. A separate molecular viewing gallery of more than 280 molecules includes rotatable 3-D structures of aspirin, caffeine, DNA, nicotine, penicillin... Requires Chime.
3-D molecular representations of alkanes, alcohols, aromatics, ketones, organic acids, poisons, drugs...requires Chime. One of the best and continually updated.
Molecules can be interactively sized and rotated. Good for alkanes, cycloalkanes, alcohols, aromatics, aldehydes, ketones, esters, ethers, alkenes... Requires Chime or RasMol.
Select 'Biochemistry Tutorials in Chime, Ready-to-Use' to select one out of over 80 sites by over 40 authors covering hundreds of topics.
Structure of Coordination compounds...Ligands, optical and geometric isomerizism. Requires Chime plug-in.
A simulator that shows how changing the conditions of an experiment alters the resulting kinetics. Options (8) include unimolecular reactions, bimolecular reactions, and a rate-limiting step reaction. The effect of temperature on the rate of reaction is clearly demonstrated
Dynamic illustrations of first and second order reactions. Initial concentrations of reactants can be adjusted to see the effect on the rate of reaction. The rate constant can also be changed.
An applet that illustrates the roles of activation energy, Ea, and reactant orientation in the rate of reaction. Dynamic graphics are simple but effective. Accompanying text is helpful.
An applet which follows the rate of decomposition of dinitrogen pentoxide at 338 K. Enter an initial concentration and observe the decrease in [N2O5] as a function of time. The initial rate is also determined graphically by the program. This is repeated at different initial concentrations and the initial rates for each [N2O5] plotted versus concentration. From the data the order, the rate constant, and the rate expression can be determined.
An applet which follows the nitrogen dioxide at 573 K. Enter an initial concentration and observe the decrease in [NO2] as a function of time. The initial rate is also determined graphically by the program. This is repeated at different initial concentrations and the initial rates for each plotted versus [NO2] or [NO2] x [NO2]. From the data the order, the rate constant, and the rate expression can be determined.
An applet that simulates first order reactions. You can change both the reaction constant or the concentration of the reactant.
This very illustrative apllet allows you to test possible chemical reactions and decide which ones can be used with Hess's Law to determine the heat of formation of magnesium oxide. It also includes enthalpy diagrams and other thermodynamic cycles, such as the Born-Haber cycle for sodium chloride.
Confusing but useful applet that features a plot of the Gibbs Free Energy Equation. The values for Delta H and/or Delta S can be changed and the temperature at which the reaction changes spontaneity appears on the x-axis.
A different way of interactively observing changes in the Maxwell-Boltzman Distribution as temperature and/or particle mass is changed. No text, no explanation with the applet. Adjust temperature and mass by initially pulling with pointer from the top of their respective columns.
A balloon is used to demonstrate the properties of the ideal gas law. Click on the thermometer column to change the temperature and view a plot of the velocity distributionof the particles in the balloon at different temperatures. Easy to use and to understand.
A six window applet that is designed to demonstrate the concept of temperatures, how pressure is related to temperature under conditions of fixed volume, and how the distribution of particle speeds depends on the temperature.
A simulation that illustrates the effect of temperature changes on the kinetic energy of gas atoms/molecules in a closed container.
Choose the number of particles and the temperature and see a simulation of the realtime effect on the Maxwell-Boltzmann distribution.
The Second Law of thermodynamics is demonstrated by a bouncing wire-mesh ball-like object -- illustrates turning gravitational potential energy into heat. Click on energy to see the real-time conversion of potential energy into thermal energy.
Be patient. The program uses a Java applet and loads slowly. There are seven experiments covering the thermodynamics of mixing gases. This is an excellent site that is best appreciated if the directions are read carefully before proceeding. It is worth the effort.
This site offers a concise index of common crystal lattice structures. A graphical representation as well as useful information about the lattices can be obtained by clicking on the structure of interest. 71 structures are included.
Requires Chime plugin to view and rotate simple cubic (sc), face centered-cubic( fcc), and body-centered cubic (bcc). Interactive exercises available to check the understanding of these three crystal structures.
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A free introductory tutorial for building, studing, and visualizing crystals. Requires a lot of work to understand how to use this tutorial but the results are excellent.
The Durham Supramolecular Chemistry Group presents the parameter Z' which is used to denote the number of molecules in the asymmetric unit. The meaning of Z' and it's limitations are briefly discussed.
Applet that graphs titration curves based on a choice of acid made from a list of acids of varying strength and a choice of base made from a list of bases of varying strength. The pH at the equivalence point is indicated on the graph and its value shown. It is interesting to plot several acids of varying strength (by not clearing graph) with the same base to see the effects of pKa on the plot.
Java applet showing titration curves being drawn for the acid of your choice... weak or strong...monoprotic or polyprotic. Non math based.
Applet that illustrates the three vibrational modes of CO2 symmetric stretch, asymmetric stretch, and bending.
A collection of Java applets illustrating quantum mechanical processes. Interactive plots of hydrogen atom probability density, Heisenberg's Uncertainty Principle, and the simple harmonic oscillator are restricted in functionality but useful learning underlying concepts.
The relationship between the wave function and probability is shown by this program. When a wave function is sketched in the Wave Function window on the screen, the program computes the corresponding probability density distribution and displays it in the Probability Density window.
Gas Laws and States of Matter
Applet shows volume change in a closed graduated cylinder as the temperature changes on an accompanying thermometer. Each time the simulation is stopped a P-T data set is generated and plotted on the included graph.
A simulation that illustrates the effect of temperature changes on the pressure of a gas in a closed container. A P-T graph would be helpful.
An applet that graphs pressure and/or temperature changes as they are made interactively for water, carbon, or MgSiO3. Changes of state due to changes p-t conditions are indicated on the plot. East to use.
May be the best view of VSEPR structures available without a plugin. Click on structure of choice and view rotating structure plus information regarding it hybridization, polarity, molecular examples…
Describes how to use VSEPR rules to predict molecular geometries. Also includes sections covering isomers, multiple bond considerations, visualizations (Chime plug-in helpful).
Includes a tutorial, 3-D (requires Chime for hyperactive rotation), examples, problems. Worth a look!
An introduction to isomerism. Requires Chime. Segments on structural isomers, chirality, stereoisomerism with one and two chiral sites, stereochemical nomenclature...
A one page primer on symmetry, handedness, and chirality. Nice large, easy to understand graphics.
Two types of exercises are provided. One involves the classification of a given molecule as either chiral, achiral, or meso. The other exercise involves the comparison of two molecules and the determination of their relationship as enantiomers, diastereomers, constitutional isomers, non-isomers, or identical compounds.
A site that provides a well-conceived stereochemical tutorial covering the some of the conventions used for the representation of 3-D molecules on 2-D surfaces and an interactive tutorial for Conformational Analysis that requires athe Chime plug-in. A molecular viewing gallery of approximately 280 molecules that are viewable using Chime is also available.
Odds and Ends
After learning how to enter the required information, you will be able to create your own 2D chemical structures (either in gif or png format). Very usefull and surprisingly quick!
A clever interactive representation of the changing amounts of the different isotopes in a radioactive series for U235, U238, Th232, and Pu241. Seen as a changing bar graph.
Click on problems to choose an unknown from a list of 64 divided between easy, moderate, or difficult to solve. Use the unknown's IR, NMR, and mass spectra to determine the identity of the unknown.
Applet that dynamically illustrates osmosis process but without any adjustable parameters such as pore size and/or molecule size. The accompanying text explanation is helpful.
Applet shows step by step sequence of the polymerization from reactants to products. A good starting place for understanding polymer formation.
This Java applet simulates the appearance of the emission spectrum of a selected element as would appear in a good visual spectroscope. The color and intensity of the lines are very good. Spectra include: Hydrogen, helium, oxygen, nitrogen, neon, iron, calcium, argon, sodium, xenon
An applications database for help in the determination of IR, NMR, and mass spect unknowns. Enter the chemical shift from an NMR spectrum and get possible structures which could have caused the chemical shift. Follow the same procedure by entering wave numbers for IR spectra, and m/e numbers from mass spect fragments.
Applet that dynamically illustrates the laser process. Basic graphics and text explanation.