Download CHEM-UA 127: Advanced General Chemistry I

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CHEM-UA 127: Advanced General Chemistry I
Notes for Lecture 21
I.
SOFT CONDENSED MATTER CHEMISTRY: BRIEF OVERVIEW
Research into the chemistry of soft condensed matter often focses on polymers, including synthetic polymers, natural
polymers, and biopolymers. Synthetic polymers are used to make plastics, elastomers, conducting polymers, liquid
crystals, and micelles that are needed for soaps and detergents to work properly. These are just a few examples.
Acidic or basic polymers are currently being designed, for example, to create new membranes for use in emerging
fuel cell technologies for use in the layer between anode and cathode for conducting protons (in the acidic polymer
case) or hydroxide ions (in the basic polymer case). Short polypeptide protein-like segments (called oligopeptides) are
being engineered for medical applications, and DNA is no longer just the secret of life but is being used to create new
nanostructures (cubes, truncated octahedra, “woven” capsids,...) that have a variety of medical and technological
applications, e.g., drug-delivery mechanisms and nanobots. Soft condensed matter chemistry and physics are very
active areas of research at present (particularly here at NYU), and the purpose of this lecture is to provide a brief
introduction to this exciting area.
II.
POLYMERIZATION REACTIONS
A.
Addition reactions
Polymerization via an addition reaction starts with an initiator of the reaction. A good initiator should be a
reactive species, such as a radical, that can easily assemble the monomers into a polymeric chain by promoting bond
formation. An example of an initiator is a peroxide, which contains a weak O−O bond that can be easily broken,
leading to radical species, as shown in the figure below: Here R and R′ are any capping group, e.g., R=R′ =H,
FIG. 1. Creating the peroxide initiator.
which would give hydrogen peroxide H2 O2 . Note that the reaction produces two radical species that are available for
polymerization reactions. Suppose we now wish to use these products to polymerize chloroethene C2 H3 Cl. The first
step of polymerization is shown in Fig. 2. In this reaction, the unpaired electron attacks the double bond, grabbing
one of the electrons to create a new sigma bond between the oxygen and the carbon. The end carbon rehybridizes
from sp2 to sp3 , and the remaining electron becomes localized on the other carbon at the end of the two-carbon chain.
This new radical species is now available for a second step of polymerization as Fig. 3 indicates. After n steps of
this reaction, we finally end up with the species show in Fig. 4 In order to avoid having a radical at the end of the
reaction, this type of polymerization requires a termination reaction step. In this case, the second initiator in Fig. 1
also produces a similar chain of length n′ . These two radical species can interact in such a way that the unpaired
electrons form a bonding pair in a sigma bond (see Fig. 5). Although this reaction produces a polymer with a defect
in the appearance of two H−C−Cl groups next to each other (a consequence of trying to polymerize chloroethene!),
if n and n′ are long enough, such a defect will likely have a negligible effect on the polymer’s properties. The same is
true for the ends, which are not part of the chlorocarbon chain.
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FIG. 2. Step one of the addition polymerization reaction.
FIG. 3. Step two of the addition polymerization reaction.
FIG. 4. Result of n steps of the addition polymerization reaction.
FIG. 5. Termination step of addition polymerization.
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Nevertheless, there are cleaner termination processes, one of which is a hydrogen transfer step from one chain to the
other. This process is shown in Fig. 6. In this case, H with its one electron bonds to the radialized carbon on the
FIG. 6. Termination step of addition polymerization via hydrogen transfer.
other chain to form a new sigma bond. The remaining electron in the former C−H bond and the electron on the
radicalized carbon on the chain that gave up its hydrogen come together to form a new π bond, giving a C=C double
bond on this chain. Although there is now a slight difference between the two chains, if n and n′ are large enough,
these small differences should have only a negligible effect on the properties of the two chains.
B.
Ion addition polymerization
The use of ionic species to polymerize has some advantages in creating polymers that do not contain the defects or
differences of those created from radical species polymerization. Ion addition polymerization is similar in the sense
that it starts with an initiator. Consider, for example, the butyl lithium species in Fig. 7 below. Suppose now we
FIG. 7. Creation of the ionic bond between butyl and lithium.
wish to polymerize ethylene to form polyethane. From the contact-ion pair state of the butyl-lithium, the first step
of polymerization is shown in Fig. 8. Note that the lone pair has now moved into the end of the carbon chain. The
process is repeated until we have a chain of length n as Fig. 9 shows. In the termination step, water is used to break
the ionic bond. This happens when a water molecule transfers a proton to the anion to neutralize it and cap off the
lone pair to give a methyl group at the end of the chain. This leaves aqueous Li+ and OH− ions in the solution,
giving, in this case, a perfect alkane chain with formula Cn H2n+2 .
C.
Condensation polymerization
As the name implies, condensation reactions, in creating a new chemial bond between monomers, also release water.
An example is show in Fig. 11, which shows condensation between two phosphoric acid molecules to give diphosphoric
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FIG. 8. First step of polymerization of ethylene using butyl-lithium.
FIG. 9. First step of polymerization of ethylene using butyl-lithium.
FIG. 10. Termination step of ion addition polymerization via proton transfer.
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FIG. 11. Condensation reaction between two phosphoric acid molecules.
acid. In this reaction, one of the OH groups on a phosphoric acid molecule combines with an H on the other, causing a
new P−O bond to form with the release of H2 O. After many such steps, polyphosphoric acid is produced, as shown in
Fig. 12. An important class of polymerization reactions that occurs via condensation is the formation of polypeptides
FIG. 12. Polyphosphoric acid.
from amino acids, which we will discuss in a subsequent section. Fig. 13 shows the condensation reaction between
two glycine molecules to form the glycine dipeptide. The Lewis structure and a snapshot of polyglycine are show in
FIG. 13. Peptide bond formation via a condensation reaction.
Fig. 14.
D.
Surface catalysis
A commonly used approach to polymerization is to employ a catalyst in the form of a reactive surface. An example
of such a surface catalyst starts with an MgCl2 support, the top layer of which is decorated with TiCl4 . When these
add to the surface, some of the chloride is washed away leaving exposed and reactive Ti binding sites. These reactive
sites possess the ability catalyze C−C bond formation. The mechanism of this is shown in simple Lewis structures
and in snapshots from a molecular dynamics simulation performed by Boero et al. J. Am. Chem. Soc. 120, 2746
(1998). These show the formation of polyethane at the Ti reactive site (see Fig. 15).
III.
MICELLES AS AN EXAMPLE OF A SYNTHETIC POLYMER
In the Overview section, we alluded to some of the many applications of synthetic polymers. One particularly
fascinating class of such applications are to micelles and reverse micelles. A micelle is a structure formed from
polymers that have a long hydrophobic tail and a hydrophillic head group. An example is sodium lauryl sulfate, an
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FIG. 14. Lewis structure and snapshot of polyglycine.
FIG. 15. Lewis structures and snapshots illustrating Ziegler-Natta catalysis in the formation of polyethane.
ingredient in many shampoos (see Fig. 16). In aqueous solution, the hydrophobic tails will be drive by hydrophobic
forces to cluster together exposing the hydrophillic head groups to the solutions. A low-energy structure for this type
of clustering is a sphere with the tails in the center and the head groups decorating the outer surface. This is shown
in Fig. 16.
FIG. 16. Sodium lauryl sulfate as an example of a micelle-forming molecule, shown together with a cartoon of a micelle.
The spherical shape of micelles is critical for their function in soaps and detergents. In water, oil and grease, which
are also hydrophobic, form droplets that want to escape exposure to water molecules, which they can do by becoming
trapped among the hydrophobic tails in the micelles. When the micelles are washed away, they carry the oil and
grease with them, cleaning clothes, dishes, hands,....
If these polymers are exposed to a hydrophobic solvent like oil, the opposite effect to that of a micelle is observed, i.e.,
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the hydrophillic head groups are driven to the center of the micelle and the tails are exposed to the oil solvent. Such
a structure is called a reverse micelle. Reverse micelles can trap small pockets of water in the center of the reverse
micelle in which small molecules such as pharmaceuticals can be trapped. In this way, reverse micelles can be used a
drug delivery devices or in other applications where small molecule payloads are needed (see Fig. 17).
FIG. 17. Cartoons contrasting micelles and reverse micelles.
IV.
POLYPEPTIDES AND PROTEINS
Previously, we showed that a condensation reaction can be used to form peptide bonds between amino acids. Living
organisms build their functional proteins using a library of twenty amino acids, which we show in the table in Fig. 18.
These amino acids are classified according to their polarity, charge, aromaticity,.... as the table indicates. Note that
these are all shown as zwitterions in which the acetyl end is negatively charged and the amine end is positively charged.
Given such a library of twenty amino acids, the number of possible sequences is atronomically large. For example,
the number of possible sequences in a polypeptide containing 100 amino acids is 20100 . Obviously, this is a far larger
number than the number of actual possible functional proteins used by living organisms. In fact, nature has carefully
engineered amino acid sequences that fold into specific three-dimensional structures intimately connected to their
function. In class, we illustrated this with the example of an enzyme, the HIV-1 wild-type protease, which folds
into a structure characterized by a hydrophobic pocket that contains two catalytic aspartic acid residues and two
loops, called the “flaps” that can open and close due to the action of a hinge-bend angle, allowing substrate access
to this active site. The flaps can close tightly around the substrate preventing escape from the catalytic pocket and
allowing the enzyme to catalyze the reactions it has evolved to carry out. Each protein folds into a unique structure
that results from its particular amino acid sequence. Understanding how proteins fold and how structure connects
to function is an active area of research. Note that the overall three-dimensional structure is characterized in terms
of its primary, secondary, tertiary, and quaternary structures. The primary structure refers to the sequence of amino
acids. Secondary structure refers to topological motifs such as helices, beta strands,.... How these secondary structure
elements pack into larger domains that constitute the tertiary structure. Finally, in multiple protein or protein-nucleic
acid structure complexes, quaternary structure arises in terms of how these individual units pack and assemble.
Some secondary structural elements are shown in Fig. 19. The figure shows an α-helix and a β-hairpin. Alpha helices
are often formed by amino acids that are nonpolar, such as alanine – polyalanine chains can form stable alpha-helices
in the gas phase. Helices are stabilized by hydrogen bonds that form between amino acids at site i and site i + 4
along the amino acid chain. On the other hand, if we create an amino acid sequence consisting of alternating polar
and nonpolar amino acids, a beta structure is more likely to form. Some different types of beta structures are shown
in Fig. 20. Research into the use of short polypeptide chains, called oligopeptides, in pharmaceutical applications is
an active area. In some of these, oligopeptides are used to bind to a immunogenic protein to provoke an immune
response. In Fig. 21, we show an example of an engineered peptide designed to mimic the action of a melanoma
antigenic peptide and provoke an immune response against this particular form of cancer (which falls under the
umbrella of cancer immunogenics). We show the peptide in two different conformations, one of which, the more
“bulged” conformation, is more active than its extended counterpart. Understanding the connection between activity
and conformation is an important issue in the design of such peptide-based therapeutics.
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FIG. 18. Table of the twenty amino acids that form the functional proteins in living organisms.
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FIG. 19. Secondary structural elements in proteins.
FIG. 20. Examples of typical beta-sheet motifs.
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FIG. 21. Examples of peptide therapeutics.