Student guide to the use of Chime

Chime, a product of MDL Information Systems, is molecular structure rendering software or freeware that operates in a browser, such as Internet Explorer or  Netscape.  You will need Chime installed as a plug-in in your browser to use this guide.  Chime uses files of coordinates or positional data from x-ray crystallographic analysis or other experimental techniques (actual measurements) and computational software packages (theoretical calculations). 

The Basics of Chime  Advanced Capabilities  Electrostatic Potential Surfaces

The Basics of Chime        

Below are the multiple display options for the S8 molecule.  The 2D rendering is the classical textbook view.

2D rendering wireframe sticks ball & stick space filled

If you place the cursor on any of the 3D structures click and drag (hold the click and move the mouse), you can rotate the molecule into any position or orientation.  Is the eight member sulfur ring planar or puckered?

Now here is a more complicated molecular structure to examine - the sucrose molecule or common table sugar.

If you right click on the molecule, a menu of items will appear as shown below on the left-side.

Under display you will find the options shown above for the S8 molecule.  Try changing the  3D display.  How would you describe the space filled version of the molecule?

If you hold the shift key down, click and move the mouse the image will zoom in or out.  This is useful to explore an aspect of a structure close up.

View the sucrose molecule in the various display modes.  The van der Waals radius is essentially the size of the electron cloud around the nucleus of the atom.  The spacefill display above produces solid spheres.

Chime uses a standard set of colors for the atoms.  If you click on an atom, its identity is shown at the lower left on your browser where a URL would show (status bar).  What element is white?               red?              gray?

The standard CPK colors for the most common elements are given below:

    C         H        O         N         P         S    
   Cl        Na        Br        Fe        Mg    UNK  

http://info.bio.cmu.edu/Courses/BiochemMols/RasFrames/CPKCLRS.HTM

The menu below shows other options that are available.  You can turn the hydrogen atoms on and off, when off they make the structure easier to view.  You can have labels on all the atoms, show H-bonds if they are part of the molecule file, and illustrate the van der Waals radii in see-through cloud forms (dots).

Show the dot surface for sodium chloride.  The dot surface allows you to view inside the structure.  How would you describe the packing of the ions?  

For biological molecules such as proteins and nucleotides, there are additional display modes that are very helpful for these complicated molecules.  Hemoglobin is shown below. 

        

For hemoglobin above, right click and select Display and then cartoons to see the helical nature of this protein.  If you right click again and select Color and then select Chain, you will see the four separate units that make up the quaternary structure of hemoglobin.

               

The Advanced Abilities - Making Measurements

Chime has the capability to measure bond distances, bond angles, and torsion angles.  Right click and go to Select and then Mouse Click Action.  Click on the function on the right you want. 

To measure a bond distance you click on two adjacent atoms in succession, the distance is reported in angstroms after clicking on the second atom.  Multiple by 100 to convert to picometers (pm).  The results are displayed at the lower left of your browser screen on the status bar.

Measure the Pt - N bond distance in cisplatin, Pt(NH3)2Cl2, given below at the left.

 

 

 

 

 


Actually Chime can measure distances between any two atoms, they do not need to be bonded to each other.  Measure the edge of the square planar cisplatin, Cl-to-Cl. 

What is the total length of the octane chain, C8H18, given above to the right? 

To measure a bond angle you click on three adjacent atoms in succession, the second being at the vertex of the angle.  The angle is reported on clicking the third atom. Measure the bond angle for Cl-Pt-Cl in cisplatin above. 

To measure a torsion angle you click on four adjacent atoms in succession.  The torsion angle is the angle between the first and fourth atom while sighting down the length of the second and third.  The angle is reported after clicking on the fourth atom.  A good animation of a torsion angle can be found at Colby College's Chemistry website.  You will need Shockwave installed to view it.

Compare the H-C-C-H torsion angle in benzene, C6H6 (left) and cyclohexane, C6H12 (right).

 

 

 

 




A rich-source of Chime molecules that can be viewed can be found at Wellesley College by Flick Coleman in Chemistry. 

Electrostatic Potential Surfaces -  These show the distribution of charge on a molecule.  Very useful in organic chemistry!

Here are some websites, including animated molecules, for further exploration:

           Structure and Bonding

           Molecules of Life

           Stereochemistry

            Molecules in Four Dimensions

            DNA        Molecular Models in Biochemistry 

            The Virtual Museum of Minerals and Molecules

            The Online Macromolecular Museum

            Vibrational Modes of Small Molecules

            Identifying Spectral Modes

            Thermal Motion of Protein Alpha Helix

Here is a sample activity using Chime.

        Cisplatin                    Worksheet (pdf)                Answers (pdf)

If you want to construct web pages that have Chime images embedded in them, see Creating Chime Web Pages in FrontPage.   ...and THANKS to MDL for Chime.

Scott A. Sinex    Prince George's Community College    8/2005