Professor Sharmaine Cady Robinson, Ph. D.
Chemistry Courses Online


About the above banner: The molecule is acetylcholine (artist’s rendering, © CCLRC ISIS Facility), an important neurotransmitter that acts in an aqueous environment in the body. Its major role in the peripheral nervous system is to activate muscles. The brain relies on acetylcholine (ACh) for the storage and recall of memory and, in part, ACh is reponsible for concentration and focus.
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Sodium Thiosulfate and Iodine




TIPS


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To determine the atom symbol and number, hold the cursor over the atom.

To find a bond length, double click on the first atom and then double click on the second atom.

To find a bond angle, double click on the first atom, single click on the middle atom, and double click on the third atom.

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Sodium Thiosulfate
(crystalline)

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Structural Properties




Questions

What is the charge on a sodium ion?
What is the charge on the one sulfur atom?

How many valence electrons are in the expanded valence shell of sulfur in the SO3 unit? Use the nonresonance structure.  Note: Each bond represents one pair of electrons.
What is the charge on the SO3 unit?
In the resonance structure of thionate ion, what is the bond order on each oxygen atom?  Note: Each solid line represents a bond order of 1 and a dashed (broken) line represents a bond order of 0.5.

What is the total negative charge on the thiosulfate anion?
How many sodium ions are needed to balance the thiosulfate charge?

Double click on O5, single click on S2, and double click on S1.  What is the bond angle?
Based on the bond angle, what is the hybridization on the central sulfur atom?
 
sp: linear (180°)       sp2: trigonal planar (120°)       sp3: tetrahedral (109.5°)

This hybridization gives what geometry around the central sulfur atom?



Double click on O5, single click on S2, and double click on O3.  What is the bond angle?
Based on the bond angle, what is the hybridization on the central sulfur atom?
The hybridization gives what geometry around the central sulfur atom?

Double click on S1 and S2.   What is the bond length?
Double click on S2 and O5.  What is the bond length?
Which bond length is shorter?




Tetrathionate Ion
(aqueous)

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Structural Properties




Questions

What is the charge on a SO3 unit?
What is the total negative charge on the tetrathionate anion?
How many sodium ions are needed to balance the tetrathionate charge?

Does the sulfur atoms in the SO3 units in tetrathionate ion have the same number of valence electrons in their expanded valence shells as thiosulfate?
Do the SO3 units in tetrathionate ion have the same bond order as the thiosulfate ion?

Double click on S1, single click on S2 and S4, and double click on S4 atoms in the S chain.  What is the dihedral bond angle?
Double click on S1, single click on S2, and double click on S3. What is the bond angle?
Based on the bond angle, what is the hybridization on a central sulfur atom in the S chain?
 
sp: linear (180°)       sp2: trigonal planar (120°)       sp3: tetrahedral (109.5°)

This hybridization gives what geometry around a central sulfur atom?



Double click on S2, single click on S1, and double click on O7. What is the bond angle?
Based on the bond angle, What is the hybridization on the central sulfur atom in an SO3 unit?
Double click on O7, single click on S1, and double click on O6. What is the bond angle?
Based on the bond angle, What is the hybridization on the central sulfur atom in an SO3 unit?
Do both measurements give the same hybridization? 
This hybridization gives what geometry around the central sulfur atom in an SO3 unit?

Double click on S1 and S2.  What is the bond length?
Double click on S2 and S3.  What is the bond length?
Is there any difference between the two bond lengths?
 

Starch - Iodine Complex
(aqueous)

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Structural Properties




Questions

What is the charge on the triiodide ion?
What is the bond angle around the central iodine atom?
What is its geometry?
What atom connects the glucose units in starch?  Note that the chain of glucose units are twisted into a helix that forms a cylindrical tube that the I3- ion slides into to form the charge-transfer complex that absorbs visible light in the 595-625 nm (orange) region.  This accounts for the blue-black color of the complex.



Jmol: an open-source Java viewer for chemical structures in 3D. 

http://jmol.sourceforge.net