Structure in Chemistry
Concepts of Acidity
AB19. Application Problems
Fraser Stoddart (Northwestern University) shared the 2016 Nobel Prize in chemistry for the development of “molecular machines”. The components of a simple molecular valve are shown here. (Adapted with permission from Nguyen, T. D.; Leung, K. C.-F.; Liong, M.; Pentecost, C. D.; Stoddart, J. F.; Zink, J. I. Org. Lett. 2006, 8, 3363-3366. Copyright 2006 American Chemical Society).
a) What structural feature do all bases have in common?
b) Which atoms in the molecules shown below could potentially be basic: F C N O Si H
Order these basic atoms from most basic to least basic.
State the reason for this order.
c) Circle the most basic site in each of the three molecules (one in the tether, one in the dye, one in the cap).
Box the most basic site of all.
State the reason for its superior basicity.
d) Modify the drawing above to show that site in its protonated state.
The tether is bonded to a silica surface. When the system is protonated, the cap remains bound to the tether (below, left).
e) What intermolecular force binds the cap and tether together?
f) Why does the dye get trapped?
When placed in water, the nanoparticles remain bright yellow and the water remains colourless. If triethylamine is added, the nanoparticles turn white and the water turns yellow.
g) After adding triethylamine, where is the dye?
h) Draw triethylamine.
Show, with curved arrows, what triethylamine does to the molecular valve. You don’t need the entire structures; you can abbreviate to just the part you are using.
i) Indicate any changes in the intermolecular forces after addition of triethylamine.
N,N-Diisopropylethylamine can also release the dye, but more slowly. Triethylamine causes the dye to be released with a half-life of 100 seconds; the half-life for release with N,N-diisopropylethylamine is 300 seconds.
j) Draw N,N-diisopropylethylamine.
k) Why is release so much slower with N,N-diisopropylethylamine?
This system has the potential to be used in a number of applications, such as drug delivery: the slow release of pharmaceuticals into the bloodstream from silica nanoparticles.
The laboratories of Teresa Reineke and Tim Lodge at U MN collaborated to study
the use of a polymer as a possible drug delivery device for gene therapy
(Adapted with permission from Laaser, J. E.; Jiang, Y.; Sprouse, D.; Reineke, T.
M.; Lodge, T. P. Macromolecules 2015, 48,
2677-2685. Copyright 2015 American Chemical Society).
Here is a section of their polymer:
These polymer chains coil up, forming spherical
a) Add any lone pairs to the structure above.
b) Show what happens to the polymer structure when aqueous HCl is added.
After treatment with HCl, the polymer nanoparticles expand, from spheres with radii of about 20 nm to spheres with radii of about 40 nm.
c) Show cartoons of a long polymer chain coiled up to form (i) a sphere of radius 20 nm; (ii) a sphere of radius 40 nm.
d) Why do the nanoparticles expand when HCl is added?
After treatment with HCl, the polymer binds DNA molecules. Here is a short section of DNA. It has three repeating units.
e) Add any formal charges.
f) Circle one sugar. Put a square around one phosphate. Put a triangle around one base (as in “DNA base pair”). Put a dashed circle around an aromatic ring.
g) Show how one of these other base pairs binds to the DNA strand.
h) One of the base pairs binds more tightly than the other one to the DNA strand. Which one? Why?
i) Why do the acid-treated polymer nanoparticles bind DNA?
Salt solutions (such as aqueous NaCl) were subsequently shown to trigger DNA release from the DNA-nanoparticle complexes.
j) Why would these conditions lead to DNA release?
Triethylamine solutions ([CH3CH2]3N) cause the nanoparticles to shrink and they also trigger DNA release.
k) Why would triethylamine inhibit DNA binding?
l) Why would triethylamine cause the nanoparticles to shrink?
Certain peptide solutions also trigger DNA release.
m) This is not the structure of a peptide at neutral pH. Modify the structure to reflect neutral pH.
n) Why would this peptide trigger DNA release?
o) This peptide would probably not trigger DNA release. Modify the structure to show why.
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