part xii supramolecular chemistry - uah - engineering xii supramolecul… · chemistry of...

Spring 2009 EE 710: Nanoscience and Engineering

Part 12: Supramolecular ChemistryImages and Charts taken from:

Hornyak, et.al, Introduction to Nanoscience, CRC press, 2008 Chapter 11

Instructor: John D. Williams, Ph.D.Assistant Professor of Electrical and Computer Engineering

Associate Director of the Nano and Micro Devices CenterUniversity of Alabama in Huntsville

406 Optics BuildingHuntsville, AL 35899Phone: (256) 824-2898

Fax: (256) 824-2898email: williams@eng uah eduemail: [email protected]

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Chemistry of NanomaterialsChemistry of Nanomaterials• Nanoscale chemistry is all of traditional chemistry +

h i t i d f t i l th i dchemistry required for nanomaterial synthesis and subsequent chemical derivatization on substrates

• True bottom up nanofabrication• Requires a solid understanding of both organic and

inorganic chemistry• Supramolecular chemistry is the chemistry of the

intermolecular chemical bond– Rooted in organic, colloid, coordination, polymer, and

biochemistriesSynthesis controlled by thermodynamic stability regimes instead– Synthesis controlled by thermodynamic stability regimes instead of kinetic control

– Solvents and entropy effects have a greater impact on the course of the reaction and overall product stability

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JDW, UAHuntsville ECE, Spring 2009

Types of Chemical SynthesisTypes of Chemical Synthesis

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Thermodynamic vs. Kinetic Ch iChemistry

• Two general types of chemical synthesisg yp y– Kinetic: conditions (including reaction times) that lead to the

reaction products in a proportion governed by the relative rates of the parallel (forward) reactions in which the products are f d th th b ti ll ilib i t tformed, rather than by respective overall equilibrium constants.

– Thermodynamic: conditions that lead to the reaction products in a proportion governed by the equilibrium constant for their interconversion of reaction intermediates formed in or after theinterconversion of reaction intermediates formed in or after the rate-limiting step

– In actuality both factors are always present in every chemical reaction

– The important note is that we are able to manipulate experimental conditions to favor a preferred product whether it is kinetic or thermodynamic

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Table 11 2 ContTable 11.2 Cont.

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Universal example: controlled addition of HBr to the double bond of butadiene

• At low temperatures, the less stable kinetic product is favored

Kinetic product

stable kinetic product is favored b/c the intermediate in the reaction goes through a pathway that requires lower activation energy.

• At elevated temperatures there is• At elevated temperatures, there is enough energy available for the reaction to proceed through another intermediate with higher activation energy that leads to a thermodynamic product

Thermo productthermodynamic product

• At high enough temperatures there is enough free energy in the system to reconvert the kinetic product back into the i t di t d th t thintermediate and then to the thermodynamic product

• Note: this example is of intramolecular chemistry and not of supramolecular chemistry, but p yit provides an excellent example of kinetic vs. thermodynamic reactions in chemistry 10


Template EffectsTemplate Effects• Kinetic parameter that is able to

influence the outcome of ainfluence the outcome of a reaction controlled by steric pathways

• Its ironic that the use of a kinetic template effect first puttemplate effect first put supramolecular chemistry on the map

– K+ cation is able to organize the assembly of a stable i t di t i t t h d lintermediate into an octahedral geometry instead of the more stable polycondensate product.

– The more reactive K+ cation bound the precurser molecule pinto a crown shaped dome leading to a Noble Prize for Charles Cram and the birth of Supramolecular Chemistry

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• Kinetic metastable materials will exist when– There are no other molecules around with which to react– The environmental conditions are able to support their stability (ie low temp)– The space remains confined (ie lack of entropy)

It becomes chemically stabilized by another reaction (ex a shell of ligands)– It becomes chemically stabilized by another reaction (ex. a shell of ligands)• Thermodynamic template effect

– Equilibrium shifts to favor a metal-stabilized product with high yield– Without the presence of the templating material, then the other products wouldWithout the presence of the templating material, then the other products would

participate in the product mixture– Thus the metal is able to exclude other reactions from occurring by forming a

thermodynamically stable productA metal cation’s ability to “select” the best ligand to form and energetically– A metal cation’s ability to “select” the best ligand to form and energetically favored complex in a reaction mixture alters the equilibrium in favor of the thermodynamic product

– Ex. Self assembly π-π stacking, hydrogen bonding

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Supramolecular DesignSupramolecular Design• Selectivity of the host-guest process is crucial in designing a large

intermolecular bonded moleculeintermolecular bonded molecule• The guest must be the best thermodynamic fit for the host of all

possible products possible in the solution• Using a lock and key fit, each supramolecular molecule has the g y , p

ability to accommodate complementary pairs until the precursor material is exhausted– Leads to large molecular systems

• Choosing both functionality and structural design is crucial• Choosing both functionality and structural design is crucial. • The guest molecule must have a binding site that is preferential to

the host while still having a functional element capable of anchoring itself to the next molecule or being used to reorganize the overall

l l h h t dsupramolecular shape when acted upon.

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Soft MatterSoft Matter• We call solid and glasses that operated under these parameters soft-matter• Soft matter has grown into an entire subfield of condensed matter physics

over the past 20 years.– Excellent textbook on the mater: Principles of Condensed Matter Physics

b Ch ik d L b k C b id U i it P 1995by Chaiken and Lubensky, Cambridge University Press, 1995

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Molecular RecognitionMolecular Recognition• Defined by the energy and the information involved in binding and selection

f b t t b i t l lof a substrate by a given receptor molecule• Mere binding is not recognition, although it is often taken as such• Recognition is binding with a purpose and implies a pattern process through

a structurally well defined set of intermolecular interactionsa structurally well defined set of intermolecular interactions

• Static Molecular recognition: similar to lock and key, involving complexation

Jean-Marie Lehn

between one host and one substrate• Dynamic Molecular recognition: Multiple hosts and guests with several

simultaneous binding sites. If a guest is bound by one site then the thermodynamic propensity to associate by another site maybe be increased y p p y y y(positive allosteric effect) or decreased (negative allosteric effect)

• Unless we are dealing with an isolated host and guest, all integrated supramolecular systems of two or more molecules exert influence on one another and the wholeanother and the whole

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Preorganization and C l iComplementarity

• Preorganization: design term involved in the selection of host and guest so that a thermodynamically stable product is based on the process

• Complementarity: state in which one component complements the structure, electronic character, and function of another component. Ie a good fit!!

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Molecular Recognition

Synthesis and Function illustrated in 4 steps:1 Covalently bonded precursurs combine to1. Covalently bonded precursurs combine to

form the repeating unit in b)2. 3 monomer units are covalently bonded to

a macrocyclic compoundy3. H-bond interactions stabilize the

confirmation for tight binding of K+4. Hydrophobic perimeter generated enables

valinomycin to become membrane solublevalinomycin to become membrane soluble

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Continuation of Molecular R i i i NRecognition in Nature

• One of the simplest pheromones• Released by a female silkworm moth and binds to protein

receptors that exist on the nanostructure of the sensillia of a male moth

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Synthesis of SupramoleculesSynthesis of Supramolecules

Clathrates: Large diverse range of compounds that formcompounds that form lattices capable of trapping guest species

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Crown EthersCrown Ethers

• Crown Ethers: O2 in aliphatic ethyl bridges to form a circular macrocycle

• Azacrowns are crowns containing Nitrogen instead of Oxygen

• Belong to the corand family which contains all of the molecular boxes and squares

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CryptandsCryptands• Cage like bicyclic molecules that

are three dimensional analogs of crown ethers

• Mixed cryptands contain other atoms besides Oxygen. The substitute is usually Nitrogen

• Amine based cryptands have an affinity for binding to Ammonium cations, alkaline earths, and lanthanides.

• The cavity is deep within the molecule, thus once bound the metal tends to remain

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CyclophanesCyclophanes• Benzene rings held together by aliphatic or amine bridges• Positive charge imparted to cyclophanes is able to enhance its

selectivity towards anionic –hydrophobic guests• Thus the molecule attracts the anion and the hydrophobic pocket y p p

provides the specific binding specificity• Size of the cavity depends on the number of benzene rings in the

structure

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DendrimersDendrimers• Cascade molecules with highly

branched 3-D structure and are oftenbranched 3-D structure and are often spherical in shape

• Subunits are relatively simple amines or other branchable molecules

f• Molecules with fractal like qualities• Three methods for generation

– Divergent• Assembled from center to the peripheryp p y

– Convergent• Assembled from the outside in

– Site isolation• Core guest from which the• Core guest from which the

dendrimer is constructed• Cores are porous and capable of

hosting other molecules First Dendrimer Synthesis techniqueFirst Dendrimer Synthesis technique demonstrated in 1985

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Hydrated methane. Used here to illustrate the importance of hydrogen bonding and its ability to form solids from liquid counterpartscounterparts

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Surfactants and MicellesSurfactants and Micelles• Surfactants are surface active agents• Hydrophobic ends of surfactants form an interface with insoluble products while at

the same time the hydrophilic ends interface with a polar solvent to render athe same time, the hydrophilic ends interface with a polar solvent to render a hydrophobic particle soluble in polar solvents

• Most common use: soaps where the ends intramolecularly bind with hydrophobic dirt• Addition of surfactants also reduces the surface tension of waterAddition of surfactants also reduces the surface tension of water

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Surfactants and MicellesSurfactants and Micelles• Amphiphiles are molecules that have polar moiety attached to one end and a

nonpolar group at the otherp g p– When placed in a polar solvent such as water they auto-allign to create a

hydrophilic surface to the solvent with a nonpolar The simplest example of an amphiphile is that of a micelle

– The critical packing parameter (cpp) is used to describe the geometrical shape of the alignment.

• A value of 1/3 indicates conical packing with tails sharpening to a pointS h h f ½• Spheres have a cpp of ½

• Cylinders have a cpp of 1• Inverted micelles are formed for cpp >1 leading to planer bilayers or

wedge shapeswedge shapes

Where V is the volume of the AmphiphilecapcapLA

Vcpp =

Where V is the volume of the Amphiphile, Acap is the area of the head-groupLcap is the length of the head-group.

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Surfactants and MicellesSurfactants and Micelles• Each micellular system is

characterized by a uniquecharacterized by a unique critical micelle concentration (CMC)

• Surfactants exist as independent molecules up until a limiting condition at the point of the CMC

• Beyond that concentration auto-allignment takes placeauto allignment takes place and micelles are formed in solution

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Biological Supramolecular Host Speciesg p p

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Biological Supramolecular Host SpeciesBiological Supramolecular Host Species

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Extended Supramolecular Structures

• Examples include large intramolecular squares• Squares bound to metallic clusters• Supramolecular Benzocorones – Liquid Crystals• Helical Supramolecular Polymers such as Ureido-s-triazines whichHelical Supramolecular Polymers such as Ureido s triazines which

can be used as chiral nanotubes

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Golden Molecular SquaresGolden Molecular Squares

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part xii supramolecular chemistry - uah - engineering xii supramolecul… · chemistry of...

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