Week10b-Phase-Transition-v2.pptx

Phase Transition –From Simple to Advance Perspective SIO1001 SEM2  Contents Phases of matter Review of phase changes Biomolecules Biomolecules’ Self-Assembly Importance of Self-Assembly Biomolecules’ Self- Assembly  Outline...

Phase Transition –From Simple to Advance Perspective SIO1001 SEM2  Contents Phases of matter Review of phase changes Biomolecules Biomolecules’ Self-Assembly Importance of Self-Assembly Biomolecules’ Self- Assembly  Outline Self-Assembly – What is it? – Forces and interactions – Examples from nature – Nanotechnology examples  What is Self-Assembly? Ever-evolving definitions Sometimes called self-organization One possible definition: a reversible process that involves pre-existing, distinct components of an initially disordered structure Therefore, self-assembly ≠ formation “Self-Assembly at All Scales,” G.M. Whitesides and B. Grzybowski, Science 2002, 295 (5564), 2418.  More on Self-Assembly Has origins in organic chemistry: structures are determined bond-by-bond, but the structures are molecules (less than about 0.5 nm in size) However, it is impossible to direct the formation (bond-by-bond) of larger nano- and micro-scale structures Self-assembly fills the processing gap by utilizing specific (usually weak) interactions between molecules to build 2- D and 3-D structures in the 10’s to 100’s nm size range “Self-Assembly at All Scales,” G.M. Whitesides and B. Grzybowski, Science 2002, 295 (5564), 2418.  Many things (living and non-living) spontaneously organize over many length scales: Å to light year. 1 Å nm mm km AU ly 10-9 10-7 10-5 10-3 10-1 101 103 105 107 109 1011 1013 1015 1E-10-10 1E-09 1E-08-8 1E-07 1E-06-6 1E-05 1E-04-4 1E-03 1E-02-2 1E-01 1E+001E+ -0 011E+021E+ 2 031E+041E+ 4 051E+061E+ 6 071E+081E+ 8 091E+101E+ 10 111E+121E+ 12 131E+141E+ 14 151E+1616 10 10 10 10 10 10 10 10 10 10 10 10 10 10  Forces at Work in self assembly Type or Scale of Self-Assembly Molecular Nano & Meso Scale Macro-scale van der Waals Brownian Motion Gravitation Electrostatics Capillary Forces Electromagnetic Fields Hydrogen Bonds Entropic Interactions Magnetic Interactions Coordination Bonds Self-assembly usually occurs in a fluid-like state. The materials (molecules or particles) should be able to move around. They sample many different orientations and interactions with respect to each other. One orientation (interaction) tends to be more favorable than others. Given enough time, the structural elements optimize their local environments to produce a self- organized structure over a large volume  Bonding and Forces Revisited Covalent Bonds Cl Cl Ionic (electrostatic) - + Hydrogen Bonding van der Waals Forces Hydrophobic Interactions Competition Between Forces Often, self assembly occurs due to a competition between two types of forces or interactions. Each type of force acts over a characteristic length scale. The table below illustrates the types of self-assembly arising from the interplay of long range repulsions and short range attractions Long-Range Short-Range Example of Self- Repulsion Attraction Organized System Hydrophobic/ Covalent Bonding Micelles, Lyotropic LC Hydrophilic Incompatibility/ Covalent Bonding Block Copolymers Insolubility Coulombic Repulsion Electroneutrality Ionic Crystals Excluded Volume Minimum Space Thermotropic LC Required Electric Field Electric Dipole Ferroelectric Domains Interaction Magnetic Field Magnetic Dipole Magnetic Domains “From Self-Organizing Polymers to Nanohybrid and Interaction Biomaterials,” S. Förster and T. Plantenberg, Angew. Chem. Int. Ed. 2002, 41(5), 688.  Examples and Applications Simple case: crystallization of a compound from solution – For example: crystals of sugar forming when a heated sugar solution is cooled – By definition, a crystal is an ordered arrangement of components. In this case, the sugar crystals are comprised of highly ordered sugar molecules – Each sugar molecule develops specific contacts with neighboring molecules in the growing crystal Example: Molecular Crystals solvent molecule (water) solute molecule (sugar) specific intermolecular growing crystal interactions Self-assembly Inspiration from Nature More complicated examples that show the power of self-assembly: DNA double helix – Consists of 2 strands of DNA – Each strand contains base pairs covalently bonded to a phosphate backbone – The 2 strands are held together by hydrogen bonding between complementary base pairs Protein folding – Proteins are polymers of amino acids – They fold into intricate 3-D structures – This is discussed on the following slides  Example: Self-Assembly in Nature Data storage on the molecular level Translation Transcription (Ribosome) DNA RNA Protein DNA sequence is the code for protein synthesis Codon: 3 adjacent base pairs of DNA that code for one amino acid in the resulting protein Side-Chain 20 possible amino acids: each has a different side-chain The side-chains have different chemical properties:  large vs. small size (vdW volume and surface area)  hyrdophobic vs. hydrophilic  acidic vs. basic  hydrogen bond donors/acceptors  ability to form disulfide bonds (Cysteine: R-SH + HS-R  R-S-S-R)  ability to coordinate to metal atoms Side-chains help guide the protein to fold into a particular structure Proteins must be folded properly in order to perform their functions Some diseases arise from mis-folded proteins  Example: Self-Assembly in Nature …-Gly-Ala-Tyr-… The terminology of protein folding amino acids bearing …-Gly-Ala-Tyr-… different side-chains Primary Structure: The order of amino acids that make up the protein. They are attached, via covalent bonds, into a polymer chain Secondary Structure: Folding of the backbone chain of the protein into sheet- like or helical structures. This occurs to satisfy the hydrogen bonding capabilities of the back bone amide linkages Tertiary Structure: Packing together of secondary structure elements to form a functional protein. Hydrophobic side-chains generally pack to the inside of the protein, while hydrophilic side-chains remain on the solvent-exposed surface of the protein. The solvent here is water  Nanotechnology Applications The mechanisms involved in protein folding are still being explored by molecular biologists But, not all examples of self-assembly are so complex In fact, scientists use much simpler versions of self-assembly all the time Many applications have found their way into nanotech processes and devices  Applications of Self- Assembly Self-Organizing System Application Atomic, ionic, and molecular Materials, optoelectronics crystals Self-assembled monolayers Microfabrication, sensors, (SAMs) nano-electronics Biomembranes, emulsions, Lipid bilayers and lipid films liposomes for drug delivery Phase-separated and ionic Nano-structured templates layered polymers Liquid crystals Displays and TVs Nanosphere lithography, Colloidal crystals photonic band gap materials “Self-Assembly at All Scales,” G.M. Whitesides and B. Grzybowski, Science 2002, 295 (5564), 2418.  Surfactants Soaps and detergents are hydrophobic tail common examples of surfactants Each molecule has a hydrophilic head hydrophobic tail and hydrophilic head Surfactants can be classified When dissolved in water, according to their head group: surfactants self-assemble into Anionic – negative charge micelles to minimize Cationic – positive charge interactions between the Non-ionic – no charge hydrophobic tails and the water Zwitterionic – both (+) and (-) The choice of surfactant depends on the application: Common soaps: anionic (good cleansing and high foaming) Baby shampoo: zwitterionic (mildness) Laundry detergent: non-ionic (lower foam and less sensitive to hardness ions) Example: Micelle and Reverse Micelle Polar Solvent (Water) Non-Polar Solvent (Oil) Oil in water Water in Oil  Example: Lipid Bilayers Polar Head Non-polar Tails Lipids are natural surfactants that self- Group assemble into cell membranes Aqueous Extracellular Environment Non-polar Membrane Interior Protein Aqueous Cytoplasm  Liquid Crystals Liquid crystals exist somewhere between a solid crystal (very ordered) and an isotropic liquid (no order) – Kind of like an organized liquid – The molecules arrange themselves so that they stack into a highly ordered pattern – But the material is still fluid-like Phase change = transition from one state (arrangement of  Liquid Crystals Two general types of liquid crystals (LC): – Thermotropic LC: change phase as temperature increases/decreases – Lyotropic LC: phase changes induced by addition of solvent (change in concentration) and temperature. Some liquid crystals have an interesting property: they rotate the plane of polarization of light. This property is used in some LCD  Example: Liquid Crystals (LC) increases/decreases Thermotropic LC: change phase as temperature Lyotropic LC: phase changes induced by addition of solvent (change in concentration) Example of a liquid Heat crystalline phase (there are many) Liquid Crystal Isotropic liquid Long range order but still no long range order behaves like a fluid  Application: TFT LCD Backlight Unpolarized Light Polarizer 1 Polarized Light Self-Assembled No Voltage Voltage Liquid Crystal Applied Applied Polarizer 2  Light Blocked  Light Passes  Example: Colloidal Crystals Similar to atomic and molecular crystals, except that the size of the building blocks are much larger and the forces holding them together are much weaker (compared to the size of the particles) Colloidal: encompasses particles that have at least one characteristic dimension in the 1 nm to 1 um range – small enough to be the subjects of Brownian motion Spheric al Colloida Colloidal Crystal l Particle Closest-Packed Colloidal Spheres White HIV Virus E. Coli Blood Cell Proteins 100 nm 0.8-2 um 12-15 um Red Blood Cell 6-8 um Colloidal Particles Nano-Scale Meso-Scale 1 nm 10 nm 100 nm 1 μm 10 μm 100 μm  Summary Colloid: refers to small size of objects; encompasses nano- and meso-scale Colloids scatter light; homogeneous solutions do not scatter light There are many everyday examples of self-assembly: soaps, proteins, LCDs Emerging nanotech applications rely heavily on self-assembling molecules, polymers, and particles Advances in self-assembly may eventually lead to true “bottom-up” manufacturing Importance of Self- Assembly  Self Assembly Biology is very good at self assembly; humans less so. Example Cell Membrane made of phospholipid molecules Lipid bilayer 29  Self Assembly and Nanotechnology – or why do Physicists care about Self Assembly? “Self assembly : creation of material from its constituent components in a spontaneous, 'natural' manner, i.e. by an interaction between the components or by a specific rearrangement of them, that proceeds naturally without any special external impetus." Also known as 'Brownian assembly. ' Example: self-assembly of proteins in protein structures (in cells) such as microtubules, actin filaments and similar. Although Image of a block copolymer: this is a individual proteins stochastically polymer with two components which will move within a cell (Brownian motion), they eventually stick to a not mix. specific place as a properly Thus the architecture of the chain forces positioned part of an ordered the organisation into lamellae. structure. "This term is not related to self- 30 assembler (or assembler) which is  Lipid Bilayers Self assembly occurs because the hydrophilic heads all point towards the aqueous phase, while the hydrophobic tails try to avoid it. Polar head group Hydrophilic This can be very effectively done by forming bilayers, with the tails sitting in the centre water of the layers away from the aqueous phase. hydrophobic Hydrocarbon tail Hydrophobic hydrophilic water Lipid membranes form this way. Many molecules behave similarly. A typical phospholipid - Such molecules are known as phosphatidylcholine amphiphiles (literally 'both loving') and turn up in detergents and 31other surface active agents, as we will see  Hydrophobic Force For the lipid molecules to organise in such a bilayer implies a significant loss of entropy. This can only occur if other changes in the system lead to an overall decrease in free energy. From the schematic it can be It might be thought this arises seen how grouping a solute from enthalpic interactions, but in molecule can increase the fact this is not so, or at least it is entropy of the solvent not dominant. molecules. The driving force arises from the This entropic driving force due entropy of the solvent molecules. to a gain in water molecules is In the unassociated state the known as the hydrophobic lipid molecules reduce the force. entropy of the solvent molecules It is very important, not just for as water organises around each lipids, but for protein structure individual lipid. too. It can therefore be seen as a 32  Amphiphiles Lipids are one class of Many amphiphiles are amphiphiles. surfactants –they have the There are many synthetic effect of preferentially ones which have the same sitting at interfaces (e.g basic property of having a between air and water or hydrophilic head group, and water and oil) and a hydrophobic tail. stabilising them, and/or The head groups may be reducing their surface polar or charged. tension. Examples In terms of understanding self assembly, synthetic amphiphiles and lipids Aerosol OTSDS behave in the same way. We need to understand under what conditions they will aggregate. And if they do aggregate into what structures. 33  Aggregation Let X1 and XN be the mole The free surfactant will be in dynamic equilibrium with its fractions of molecules in monomer form and micelles of aggregates. size N respectively. The chemical potential of all Rate of association (forward identical molecules in reaction) = k1X1N different aggregates must Rate of dissociation = kN(XN/N) be the same at equilibrium. where kN is the reaction rate for the Nth order association process. Thus, recalling the chemical potential for a species of concentration c in a solvent k1 kN where the first term represents the change in free energy on taking the molecule from the bulk into solution, and the second arises from entropic 34 considerations,we can write an  States of Aggregation for Amphiphiles The diagram shows common states of aggregation. Also marked in are the building blocks for each aggregate. a It can be seen that the differences lie in le – The area of the head group a – The effective length of the tail le The planar bilayer which make up cell membranes is only one example. But first we need to understand why aggregation should be thermodynamically 35 favoured at all in a more  Packing and Shape of Aggregates We have also to consider the Example: spherical micelle packing constraints on the For radius R, the mean hydrophobic tails. aggregation number M is given by They will occupy a volume v, are assumed to be fluid and incompressible, and have a maximum effective length lc. Giving R = 3v/ao. This maximum length is Physically must somewhat empirical, and have R lc corresponds to the length beyond which the chains can no longer be regarded as fluid. Hence Given ao, v and lc (all measurable/ estimable quantities), the shape into Different molecules, with different which the lipids pack can be geometrical ratios, will therefore determined. favour different shaped micelles, Given different possible as seen on previous diagram. 36 arrangements with  Shape Changes and Fluctuations So far we have described The cell membrane equilibrium shapes for micelles. thickness is typically a few Now consider vesicles (the nm, whereas the overall equivalent term for lipid based dimensions of the cell, aggregates) as models for cells. vesicle or micelle is 10- Typically these are much larger 100mm. than micelles. A key property of lipid membranes is their ability to 10mm fluctuate. However such fluctuations cost energy as the molecular packing deforms away from its optimum. 10mm This gives rise to the idea of curvature elasticity. This elastic energy is dominant over surface tension effects, because the number of Many different types of molecules is fixed. shape changes are seen to Shape changes occur with occur due to thermal constant surface area and fluctuations. 37 volume. Example: Phase Diagram for Soaps We have seen there can be different aggregate shapes under different conditions. We can map out phase diagrams delineating the different phases. These same arguments apply for the different phases of synthetic surfactants, 'natural' surfactants such as classical soaps, or for bilayer systems. Curvature elasticity also has a key role to play in determining the equilibrium phase diagram. The phase diagram for soap is very complex. Only parts of this are actually useful when it comes to getting us clean! 38 Example: Phase Diagram for Soaps 39 Ternary Phase Diagrams – Surfactant/oil/water Slice through a three dimensional diagram Representatio n at constant T Many different possible phases 40 Self Assembly of Viruses: Example TMV 41  Aaron Klug Nobel Prize winner 1982 for his work on TMV 1926-2005 Worked with Showed just how complicated the Rosalind Franklin TMV self-assembly story is. (1920-58) on TMV Subsequently also was very up till her death. involved (at the Laboratory for Molecular Biology at Addenbrookes) with the use of electron microscopy to 42 complement X-ray diffraction. Self Assembly and Hierarchical Structures in the Cell 43  Summary Phases of matter Review of phase changes Biomolecules Biomolecules’ Self-Assembly Importance of Self-Assembly Thank you.