Self Assembly How Nature Builds Designing a model illustrates the basic ideas of self assembly S M Gail Jones Michael R Falvo Bethany Broadwell and Sharon Dotger elf assembly or spontaneous assembly is a process in which materials build themselves without assistance Goodsell 2000 This process plays a central role in the construction of biological structures and materials such as cells viruses and bone and also in abiotic processes like phase transitions and crystal formation The principles of self assembly help describe how speci c binding events occur in nature How a virus binds to a cell how an enzyme catalyzes a biochemical reaction or how a drug nds its target These principles also point toward a new era of advanced materials that build themselves as well as new drug delivery and biomedical diagnostic technologies Here we present a simple in class exercise that underlines the basic principles of self assembly and helps students understand how the scale of molecules and atoms is different than the human scale world Campbell Freidinger and Querns 2001 Principally the activity illustrates that nanoscale objects are always moving around thermal motion and that they tend to stick to each other intermolecular bonds The exercise is also a design project in which students use their imagination in concert with the basic rules of self assembly multiple weak bonds and lock andkey to produce complex self assembled models Magnets e g ceramic permanent magnets from Edmund Scienti cs or craft stores or Velcro can be used to model the sticky intermolecular bonds Legos cardboard or other building materials can be used as the body of the model 54 The Science Teacher Background information Molecular self assembly takes place at a very small scale the nanoscale A nanometer is one billionth the size of a meter The thickness of a single hair is 50 000 nm Most students have dif culty conceptualizing objects this small Developing an understanding of scales outside human sensory experience is important because many of the new frontiers of science such as nanoscience astronomy or genetics require an understanding of these scales For additional activities and explanations of nanoscale visit Nanoscale Science Education http ced ncsu edu nanoscale Intermolecular bonding Stickiness Bonds between molecules or intermolecular bonds are much weaker than the interatomic chemical bonds typically emphasized in introductory chemistry classes covalent ionic metallic Intermolecular bonds are so weak that individual bonds between molecules are very likely to dissociate spontaneously at a very high rate Hydrogen bonds between water molecules are such bonds Even though they are the strongest of the intermolecular bonds hydrogen bonds are weak enough that they are created and broken continuously In liquid water no two water molecules stay bonded together for even a billionth of a second as soon as one is broken another is quickly made Besides hydrogen bonding other types of intermolecular bonding include van der Waals forces hydrophobic interactions and dipole dipole bonds Alberts et al 2002 The origin of these and other intermolecular bonds resides in the polar or polarizable nature of molecules Some form of attractive intermolecular bonding will occur between any two atoms or molecules though it can be quite weak The weak nature of these bonds is crucial to their ability to drive self assembly Fitting the pieces together On the scale of atoms and molecules everything is shaking and bumping around very quickly due to thermal energy the higher the temperature the more bumping and shaking This ambient energy makes individual molecular bonds unstable They do not last long Instead of one very strong chemical bond sticking pieces together nature uses several weak intermolecular bonds in parallel When the pieces t properly all of these bonds work together like many hands joining and make the overall bonding stable If some bonds are made in the incorrect geometrical arrangement the pieces are only loosely bound and unstable This serves as an error correction mechanism Geometrical compatibility plays an important role in the self assembly The pieces t together like puzzle pieces The multiple weak bonds only come together when the pieces t correctly For example proteins are shaped in a very precise way to t together speci cally with other proteins to perform a task or build a structure within the body Along with the lock and key compatibility the protein will have a code of sticky spots that will correspond to the similarly sticky spots of the partner protein The binding event will be stable if the parts t together in the correct way in free energy G is negative it proceeds to a lower free energy G is equal to the change in enthalpy H minus the change in entropy S multiplied by absolute temperature T In the process of self assembly just as in the case of water freezing the change of enthalpy is negative H 0 exothermic because bond formation releases energy and the change in entropy is negative S 0 more order because the assembled structure is more ordered than the unassembled particles As the temperature rises the second term T S becomes larger and more negative and T S becomes more and more positive because of the negative sign until G is positive A positive G means that the process is energetically unfavorable The pieces will not assemble or if already assembled at a lower temperature they will come apart or melt The point at which the green line in the graph crosses the zero energy axis can be thought of as a freezing melting point or the point where self assembly becomes favorable unfavorable Note that the process depicted in the gure can be directly related to the formation of complex biomolecules for FIGURE 1 Thermodynamics of self assembly The analogy Its utility and limits In the following modeling activity Legos represent the particles themselves The magnets or Velcro act as the weak bonds to hold the particles together The reaction chambers keep the particles close enough together to increase the likelihood they will hit each other with the right orientation The shaking simulates the temperature or the kinetic energy Stressing this point with students reinforces kinetic molecular theory which states increased temperature increases molecular motion With just the right temperatures molecules collide with the right amount of energy for the coordinated bonds to form and remain stable while the undesired bonds are