Self-Assemblies, Folding, and Properties of Perylene Monomers, Oligomers, and Polymers - Molecular Self-Assembly: Advances and Applications - page 181

The code phenomenon can be explained as follows: Weak

π

-stacking force brings the monomers together via dynamic self-
assembly. (The self-assembly enthalpy

∆ H

was determined to be

SA

− −

negative, 3 7 kcal/mol, in the planar units [38,61] and smaller

∆ H

in the twisted units.) Negative helps compensate the self- SA

(also negative), thus bringing some perylene
units within 3.5 A of each other, a favorable reaction environment.
The efficaciously reduced assembly entropy pays at least partially
the disulfide-bond activation entropy-penalty

assembly entropy

∆ S

SA

∆ S

‡ S

. The perylene
template locates the TEG chain ends near each other so that the
thiol-reactive intermediates can react favorably to form disulfide
bonds. Thus, the reaction rate is greatly increased, resulting in the
kinetically favored homochiral cyclic dimer when the self-assembled
monomers have complementary molecular codes. Heterochiral
monomers also have a complementary molecular code; however,
the heterochiral molecular code directs a different self-assembled
structure, which leads to the linear dimer formation rather than
the cyclic dimer. If the molecular code is noncomplementary, such a
specific reaction rate enhancement is absent.
To increase the rate, it is desired to make the disulfide-bond
activation entropy

−

S

‡ S

as close to zero as possible. Dynamic
self-assembly reduces the number of independent molecules, with
a consequent loss of three translational and up to three rotational
degrees of freedom, albeit partially compensated by residual degrees
of freedom in the self-assembled structure, especially in the flexible
TEG chains. The perylene assemblies likely provides catalytic
factors of 2.4

∆ S

−

S

−

6.0 kcal/mol, typical of other enzymic or chelate rate
accelerations [62]. Thus, self-assembly induced diminishment in
∆ S

‡ S

significantly favors coded structure formation over random
collision products.
The self-assembly directed disulfide bond formation is quasi-
catalytic, but there is no catalyst by definition, as dynamic self-
assembly is a phenomenon not a substance. Catalysts are frequently
associated with lowering the activation

−

S

enthalpy , while activation

entropy is often overlooked. The importance of activation enthalpy

versus entropy is still highly debated; evidence supports that either
entropy or enthalpy dominates the catalytic effect in many enzymes
[63

65]. A popular alternate explanation is that self-assembly
stabilizes the encounter complex, holding the transition-state thiol
intermediates long enough to improve probability of proceeding to

−