Advanced Organic Chemistry II - Department of Chemistry ...

Chem 512 Molecular Recognition H. D. Roth

Advanced Organic Chemistry II

Chemistry 412/512 Spring 2012

Molecular Recognition

Host-Guest Interactions
Multiple Bonding

Binding Isotherm – Experimental Methods
Crown Ethers

Molecular Recognition
non-covalent association between receptor & substrate
enzyme – substrate
antibody – antigen
neuroreceptor – neurotransmitter

How do molecules of life associate and perform
Origins and energetics of binding interactions
Thermodynamics of binding phenomena between a host (H) and a guest
(G) – association constant, Ka, dissociation constant, Kd,

DimensionM–1, mM–1, mM–1,but note that ln Ka does not have a unit

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Chem 512 Molecular Recognition H. D. Roth

Quantities of [H], [G], and [H•••G] are concentration dependent

[H] + [G] have twice the degrees of translation and, hence, a greater entropy

than [H•••G]; therefore dilution favors [H] + [G]

Energetic consequence of multiple binding interactions for a single molecular

“complex”

Binding forces, dipolar attractions, hydrogen bonding, π affinities, though

individually small, may combine to result in a large stabilization; effects are not

simply additive, but have a (positive or negative) cooperativity component

the binding of A––B will be more favorable than the binding of A and B
separately because only one set of translational and rotational freedom degrees
are lost as a result of A and B being linked)

Vancomycin, a macrotricyclic antibiotic forms various H bonds, illustrated for
two D-alanine units, with the cell wall of a bacterium 0-2 kcal/mol for each H
bond
Enthalpy–Entropy Compensation
The sum of entropy and enthalpy terms often are temperature independent

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Chem 512 Molecular Recognition H. D. Roth

Explanation: weak bonding (ΔH°) still allows considerable motion (greater

TΔS); once the bonding gets stronger the mobility decreases

Binding Isotherm

A reaction tool to measure binding constants. The theoretical change in

[component] as a function of [another component] at constant temperature

Concentrations measured by NMR, UV/vis, IR and fit to theoretical binding

isotherm

1 : 1 interaction only considered

Keep one concentration, e.g., [H], (nearly) constant, vary [G]

Initial concentration [H]o; with added [G] H is distributed between free H and

H•••G; thus [H]o = [H•••G] + [H]

Note that [G] is not the amount of G added ([G]o) but the amount not
incorporated into H•••G;
Therefore, [G] has to be expressed in terms of [G]o; if [G]o >> [H]o we can
assume that[G] = [G]o, because only a small fraction of [G]o is incorporated;

A plot of [H•••G] vs., [G]o/[H]o shows: at high [G]o the adduct [H•••G]
approaches [H]o

saturation behaviour

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Chem 512 Molecular Recognition H. D. Roth

For Ka = 10 M–1, starting with 100mMol H and 10 mM [G], the equilibrium lies
at [H] = 95 mM, [G] = 5.1 mM, and [H•••G] 4.9 mM
For Ka = 10 M–1, starting with 100mMol H and 1 mol [G], the equilibrium lies
at [G] = 910 mM and [H•••G] 90 mM (most of H is complexed)
Predicting at what concentrations saturation behaviour will set in?

For [H]o = Kd and [G] << Kd, Kd + [G] ~ Kd and [H•••G] = [G]
For [H]o = Kd and [G] >> Kd, Kd + [G] ~ [G] and [H•••G] = [H] o

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Chem 512 Molecular Recognition H. D. Roth

Given Ka = 1 M–1, 10 M–1, 100 M–1: with higher binding constant it takes lower
[G] to achieve saturation
When 1/Ka is much below [H]o, the curve is quite flat
In practice use Ka ~ [H]o
Cooperativity in Protein Ligand Interactions

Hemoglobin has four binding sites for molecular oxygen
Binding at one site makes the binding at the next site more favorable (allotropic
effect). Saturation value S if all sites are occupied; with large Hill coefficient,
nH, we have steep rise in binding with minimal change in ligand concentration
(remember titration?)

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Chem 512 Molecular Recognition H. D. Roth

Experimental Methods

[H•••G] is measured by some a) chromatographic, b) electrochemical, or c)

spectroscopic method; signal intensity is related to [H•••G] by a proportionality

constant; typically we do not know these, nor do we know Ka.
Therefore, theoretical curves for proportionality constant and Ka are compared
to experimental result for best fit.

Timescale of the measurement is of utmost importance

Because the binding forces are much smaller than actual bonds, these systems

are dynamic

Rephrase the complex (adduct, assembly) equations:

Estimate of rates constants: kon diffusion controlled (kd); for an accessible host
site and a small guest, kd ~ 109 M–1s–1;
For a “reasonably strong” complex, kd will be near 10 mM,
resulting in a koff ~ 103 s–1
and a lifetime, t = 1 /koff ~ 1 ms
If the technique is faster than the lifetime, t, we can observe individual signals
for H, G, and H•••G
If our method is slower than the lifetime, t, we will observe averages
Lifetime of UV/vis or fluorescence?
Rapid observation
range: absorption: ps or faster
Fluorescence: ns or faster
Conclusion: Optical methods are well suited

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Chem 512 Molecular Recognition H. D. Roth

Benesi-Hildebrand Method

Hosts and guests have very different spectra; if one component (H) is tranparent

in the spectral range being monitored (by A or E), we have to deal only with G

and H•••G (one fewer unknown)

Lambert-Beer law


 insert binding isotherm

If [H] = [H]o (correct only if [G]o << [H]o), a doubly reciprocal plot of 1/ΔA vs.
1/[H]o gives a straight line: Δε can be calculated from intercept, Ka calculated
from slope
NMR technique: complexes (adducts) often have large values of Δδ;
Therefore, NMR is a powerful tool for host-guest complexes
Problem: timescale of NMR is slow compared to the on-off rates
We observe a signal “G”, a weighted average of G and G•••H
the shift of G•••H is unknown (an additional unknown constant)

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Chem 512 Molecular Recognition H. D. Roth

Isothermal Calorimetry

NMR and UV/vis methods provide an equilibrium constant, Ka; from Ka we

derive ΔG;

for information about ΔH, and TΔS, we can measure Ka at a number of different

temperatures and analyze a plot of 1/T vs. ln Ka (Arrhenius plot)

Isothermal calorimetry provides ΔH and Ka in a single experiment, giving

access to ΔG and TΔS as well

What is isothermal calorimetry?

Measure the heat changes upon addition of small quantities of G against addition

to a blank solution (eliminating heat of dilution )

Isothermal Calorimetry

The total heat change, Q, upon formation of H•••G is related to ΔH, the volume,

V, and the concentration [H•••G]


 Express [H•••G] in terms of binding isotherm

Host Guest Interactions
Complementarity
A concept to select host and guest with “matching” structures
Preorganization
Having a host with a fixed structure complementary to guest
Preorganization optimally realized in crown ethers

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Chem 512 Molecular Recognition H. D. Roth

Bonding by charge dipole interaction
Discovered by Peterson in 1967, pursued by Lehn and Cram
Crown Ether Complexes

Incorporation of additional water molecules: DHo gets progressively lower
whereas DSo actually increases,
to build K(H2O)6+ will have a very high entropy cost
to construct the K(R2O)6+ array from [18] crown-6: because of the
preorganization there is a significantly reduced entropy cost, making for a
stable complex
(the entropy “penalty” is “paid” during the synthesis of the crown ether)

Template Effect in Crown Ether Synthesis
Crown ether (macrocycle) synthesis is difficult because the meeting of the two
ends has a high entropy cost

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Chem 512 Molecular Recognition H. D. Roth

Synthesis is facilitated by the potential guest, as successive Os are ”wrapped

around the “template”, K+

Templated Synthesis of Crown Ethers

Because of different ionic radii different alkali ions have different efficiencies
as templates
Each alkali ion is optimally suited for one particular crown ether.

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Chem 512 Molecular Recognition H. D. Roth

Effect of Preorganization on Binding Power

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Chem 512 Molecular Recognition H. D. Roth

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Chem 512 Molecular Recognition H. D. Roth

Triaza Crown Ethers

An [18] crown-6 ether containing alternating N and O is an optimal binder for

ammonium ions

Cryptands
Rb+ incorporated in a three-dimensional cryptand containing of two N atom
bridgeheads bridged with three
(CH2)2O(CH2)2O(CH2)2O branches

For specific applications other host molecules have been synthesized, e.g., the
cleft or tweezer molecules shown

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Chem 512 Molecular Recognition H. D. Roth

Peptides may have helical structures; a 21 amino acid peptide bearing an [18]

crown-6 on every third amino acid forms an ion channel for transport of K+

Spherands

Crown Ethers and Organic Reactivity
Recall the use of crown ethers to dissolve salts in aprotic media for optimal SN2
reactions

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Chem 512 Molecular Recognition H. D. Roth

DNA Bases

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