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Chemistry 11


Molecular Simulations below
  Chapter Page

Animation/Simulation

  1 25 Periodic Table trends and atomic structure
How Orbitals fill up - Periodic Table
Webelements
Atom Builder activity
  2 47 How atoms combine
Chemical Kinetics Simulation
Ionic and Covalent Bonding animation
A visual simulation of a Chemical reaction 
  3 all Chemical Reactions
Virtual Chemistry Laboratory
Stoichiometry
Equilibrium
A visual simulation of a Chemical reaction 
Chemical Formula -->Mass
Acid-base titration
Reaction (Reactants/Products)
  4 135 Calculating Mass
Practice converting Moles to Mass and vice versa
  4 139 How to determine Molecular Mass
Formula To Mass To Formula Conversions
  4 159 Decomposition Reactions
A titration to show how unknown examples are identified
Limiting Reagents
  4 161 Experimental Error Simulation
Measurement and Uncertainty
Sources of Experimental Error
  5 172 Calculations Involving Reactions
Stoichiometry
Reaction (Reactants/Products)
  5 197 How Nuclear Reactions work
Nuclear Fission Animation
Radioactive Decay Series
Law of Radioactive Decay
Operate a Nuclear Power Plant
  6 230 Why Do Many Ionic Compounds Dissolve in Water?
How dissolving works
Solubility Applet
  8 343 Ideal Gas relationship
Molecular Model for an Ideal Gas
Pressure Chambers
Special Processes of an Ideal Gas
Maxwell Distribution --Properties of Ideal Gas Law
` 8 348 The Kinetic Energy of Gas Molecules
Kinetic-Molecular Theory
Molecules In Motion 
Gas Molecules Simulation
  8 369 Gas Mixtures
The Evaporation Laboatory
  9 409 The Antarctic Ozone Hole
The formation of Ozone
The problem with Polar Stratospheric Clouds
  10 445 Structural Isomers
Structural Isomerism
Stereochemistry
Isomer Exercise
cis and trans Isomer Exercise
  10 453 Cycloalkanes
Manipulate 3-D models of Cycloalkanes
  11 505 Petroleum Refining
How Petroleum Refining Works

Molecular Simulations:

This page contains links to interactive three-dimensional displays of some of the molecules you will study.

You may observe the many thousands of molecules available on the web using a stand alone viewer program, with Netscape browser or Internet Explorer Browser

You can construct and manipulate your own molecules, download a sample set of molecules or find molecules on the web to display

Standalone Viewer

The best free 3D molecule viewer is WebLab Viewer Lite from Accelrys. Go here to register and download the program and a file of sample molecules.

Netscape Browser Plugin

In order to view these displays, you must have the Chime "plugin" for your web browser. Chime is available free from MDL Information Systems. Chime is currently available for only Netscape Navigator  for Windows, and for Netscape Navigator on the Macintosh. Internet Explorer will not work properly
To learn about Chime and obtain the latest version, see: www.mdlchime.com

Internet Explorer Plugin

Until recently, both Netscape and Internet Explorer supported Netscape plug-ins. With the August 2001 release of Internet Explorer 5.5 SP2, Microsoft has ceased support for the Netscape plug-in format. If you are using Netscape, or Internet Explorer 5.5 SP1 or earlier, you can use the Chime plug-in. Users of Internet Explorer 5.5 SP2 or Internet Explorer 6 MUST use the ActiveX Control instead.

Though users of Internet Explorer 5.5 SP2 or Internet Explorer 6 MUST use the ActiveX Control, users of Internet Explorer 5, and 5.5 SP1 may want to use it as well. Installation is more involved, because it necessitates installing two programs (both are free, but require registration). However, this option also provides a much more powerful online and offline molecular viewing package.

    Steps to Install the ActiveX tool:

  1. Download and install WebLab Viewer Lite. This program is also an excellent stand-alone molecular viewer. The ActiveX Control won't work unless this program has been installed FIRST! Be sure to download the FREE version (Lite).
  2. Download and install the WebLab Viewer ActiveX Control.

Where do I find molecules to view?

There are many molecules available on the Internet that can be viewed in Chime. Use the search interface at http://pdblite.org for finding macromolecules. Step by step instructions on how to save a PDB file so you can view it in Chime. Updated weekly.
You can got to Chime Resources at UMass and explore many links to sites offering molecules.
Each of the links below will open up a new Netscape browser window with a display of the indicated molecule. Or download all the molecules as a zip file

After Loading: rotate the molecule by placing the cursor in the display box, click the mouse and drag. If you click on an atom in the display, the identity of the atom will appear in the message bar at the bottom of the browser window

Water
diamond
water/dimer
ice
water
water_box

Sugars

d_galactose
d_glucose
d-mannose
d-xylose
fructose
l_glucose
sucrose

Lipids

arachidonic
dlpe
linoleic
oleic
palmitic
stearic
 

Carbon

graphite
fullerene
graphite
buckyball-c60

DNA, RNA & nucleic acids

adenine
amp
atp
cytosine
dna
guanine
gtp
thymine
trna
uracil

Amino Acids

alanine
arginine
asparagine
aspartic_acid
cysteine
glutamic_acid
glycine
histidine
isoleucine
leucine
lysine
methionine
phenalalanine
proline
serine
threonine
tryptophan
tyrosine
valine

Drugs & Hormones

adrenaline
aspartame
aspirin
azt
barbiturate
caffeine
cisplantin
ibuprofen
nicotine
streptomycin
taxol
taxol
thc
valium
zantac

Build your own molecules:

ACDChemSketch and ACD/3D are free downloads from ACDLabs. With these two programs you can build any molecule [many molecule templates come with the package]. Once completed your molecule can be viewed and rotated in 3D.

 

Last Modified 01/16/2002