Module 4 - NUCLEOSYNTHESIS: FORMATION OF ELEMENTS

 1980: Carl Sagan (well-known physicist) said in his TV series Cosmos, “The cosmos is also within us, we're
made of star stuff.”
 Scientists agree with this statement because there is a lot of evidence pointing to the chemical elements
in the human body, and all the elements around us and in the universe have their ultimate origin in
stellar cosmic events.
 Stars are factories for new elements. As they live and die, they form almost all of the elements in the periodic
table. These elements make up Earth — and us.

4.1 Nucleosynthesis
 There are a little over a hundred elements in the universe. The Russian scientist, Dmitri Mendeleev
ingeniously organized these elements in the periodic table by their properties.
 Composition of the Universe:
 Hydrogen (lightest element) – 73% of all the mass of the Universe
 Helium atoms – 25%
 A meagre 2% makes up the remaining material in the universe
 What is surprising is that:
 atoms account for only 12% of the Universe
 that most of it, some 72%, appears to be made of a mysterious, invisible substance, called dark matter
 Composition of the Earth:
 Oxygen – accounts for 49.5% of the total mass of the Earth’s crust, waters, and atmosphere
 Remaining elements:
o Silicon – 28%
o Aluminum – 8%
o Iron
 lightest element, hydrogen comes in tenth
 Nucleosynthesis is the study of nuclear processes responsible for the formation of the elements― the fusing
of nuclei.
 Three types:
o Big Bang
o Stellar
o Supernova
4.1.1 The Big Bang Nucleosynthesis
 first stage of element formation started in the Big Bang, and is thus called the Big Bang nucleosynthesis
(abbreviated BBN, also called primordial nucleosynthesis).
 BBN is believed by most cosmologists to have begun about 10 seconds to 20 minutes shortly after the Big
Bang, when the universe had cooled sufficiently (from 1032 Kelvin to approximately 109 Kelvin) to form
stable protons and neutrons.
o During this short period, protons and neutrons fused to produce the
lightest elements, in particular, the hydrogen (H-1, 1H), its isotope
deuterium (D, hydrogen 2, 2H), the helium isotopes He-3 (3He) and
He-4 ( 4He), and the lithium isotope Li-7 ( 7Li). In nuclear fusion,
smaller nuclei collide to make larger nuclei, and energy is released in
the form of electromagnetic radiation.
o In addition, two unstable or radioactive isotopes were also produced:
tritium (T, hydrogen-3, 3H); and the beryllium isotope beryllium-7 ( 7Be); but these unstable isotopes
later decayed into 3He and 7Li.

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  After the next half hour (when lithium-7 was created), the universe cooled and expanded to a point
where fusion of heavier elements is deemed impossible.

4.1.2 Stellar Nucleosynthesis

 In Module 3, we learned how the light elements eventually merged into loosely knit nebulas which then
condensed to form the stars. Clustering of these stars later formed the galaxies. Interwoven with this
evolution of stars and galaxies is the formation of other elements from helium to iron ( 56Fe), in a
process known as stellar nucleosynthesis.
o Element formation by this mechanism stops at the element iron, 56Fe because the masses of nuclei
heavier than iron are greater than the masses of nuclei that are merged to form them.
o Iron has such a tightly bound nucleus that there isn't further fusion once that point is reached.
Without the heat of fusion, the star collapses and explodes in a shockwave.
 A star is a very hot ball of gas or a “nuclear fire”.
o creates elements by combining lighter nuclei into heavier nuclei via nuclear fusion reactions in their
cores, in the process releasing energy in the form of electromagnetic radiation.
 That’s why they shine! They are natural nuclear reactors!

4.1.3 Supernova Nucleosynthesis

 Forming heavier nuclei from a cooler universe and larger space is difficult. This type of event happens
only on supernovae, or stars that explode upon death.
 supernovae are important in providing the energy needed for the fusion reactions required in the
synthesis.
 Supernova are distinguished on the basis of spectral emission
 Two Types: Type I and Type II

Type I supernova
o typically occurs in white dwarfs
o While the exact mechanism is unclear, one explanation is that the white dwarf reignites carbon
fusion, which leads to a rapid nuclear fusion chain reaction that releases energy, resulting in a
supernova.
o characteristically have no hydrogen-emission line

Type II supernova
o occur in active stars that undergo core collapse and a subsequent rebound and explosion
 When the core of this star consists entirely of Fe and the inward gravitational pressure is greater
than the outward thermal pressure (from nuclear fusion), the star undergoes core collapse
 In this, the star actually implodes on itself, pushing all the atoms closer together and resulting in
electron degeneracy (where electrons are in the same energy levels).
 When this occurs and a star is smaller than 1.44 solar masses, the star then experiences rebound
(so that the electrons can maintain different energy levels)
 This causes the entire star to rebound, sending out a shock wave, which then releases energy
and results in a supernovae Type II explosion.
o are important for stellar nucleosynthesis because elements heavier than Fe can only be produced in
this manner
 the formation of elements heavier than Fe require an energy input (and therefore are not energy
generating); this energy is provided by the explosion

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  The elements form through neutron and proton captureprocesses. This large output of energy
causes the formation of many different types of nuclei, but eventually only the stable nuclei
remain. These are shown on the Valley of Stability.

4.2 Nucleosynthesis and Abundance of the Elements in the Universe

 The elements are classified based on their atomic number, or the number of protons in their respective
nuclei.
 For a certain proton count, there may be different number of nuclei
 These different versions of the same element are called isotopes
o isotopes are atoms with the same number of protons but with a different number of neutrons.
 The number of nucleons affects the properties of the elements, most especially their abundance. The
protons and neutrons contribute to the element’s nuclear stability, while the electrons contribute to its
chemical properties
 Can we manufacture elements? (TedEd)
 Hg
 The heaviest elements, those at the bottom of the periodic table, are created by man.
 they were artificially created by accelerating relatively heavy nuclei in particle accelerators and colliding
with each other at immense speed and incredible force
 The collision creates heavy nuclei, which usually are not stable and fall apart in a fraction of a second.

4.3 Nucleosynthesis and Nuclear Stability

 Nuclear stability is defined as the ability of the element to retain its current nuclear state given a certain
time interval.
 Some elements have very stable nuclei; some have nuclei that are unstable, but which decay slowly; and
some have highly unstable nuclei that disintegrate almost as soon as they form.
 This stability is affected by the relative positions, or energy levels, of the nucleons.
 However, it is common practice to relate the relative number of protons and neutrons to the overall
stability of the nucleus, thus the existence of the belt of stability.
 The stability of a nucleus is determined by the ratio of neutrons to protons.
 Unstable nuclides are subject to radioactive decay.

Conclusion
 Nucleosynthesis can be classified into two events: Big Bang nucleosynthesis (the formation of lighter nuclei
from the first moments of the universe) and stellar nucleosynthesis (the formation of post-iron heavy nuclei
from supernovae and nebular dusts).
 The reactions that take place in nucleosynthesis require a very high temperature, which is characteristic
of fusion reactions.
 These events are responsible for the existence and the current distribution of the chemical elements
throughout the universe
 The elements are composed of three different subatomic particles: the proton, the neutron, and the
electron
 The relative amounts of protons and neutrons in each element affect the element’s nuclear stability, while
the positioning and number of electrons in the element affect its chemical stability
 These parameters are responsible for almost every property of each element in the periodic table — its
existence, relative amount in the universe and the earth, and its interaction with other elements, among
others.

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4-V1 Nucleosynthesis – Breakthrough Junior Challenge 2017 (Peyton West Finch)
 How are elements created?
 Through Nucleosynthesis
 Nucleosynthesis
 The formation of elements that naturally occur
 3 Types – these nucleosynthesis are part of the formation and evolution of the universe
 Big Bang
o Occurred 13.8 billion years ago
o Is a theory which states that the universe started from a massive explosion
o 1 minute later, helium hydrogen, and lithium were created
o Clouds and gas accumulate which was the only matter in the universe for millions of years
 Eventually became stars
 Stellar
o Responsible for the creation of the elements between helium and iron in the periodic table
o Uses fusion to create elements in the center of stars
o Fusion uses extreme heat and pressure to mesh smaller elements together forming larger ones
o The extremely high heat creates heavier elements
o Fusion happens in stars till they reach iron as it is the limit because there is not enough neutrons in
stars’ cores to continue
 Supernova
o Two key characteristics during a supernova explosion, extreme temperatures and an abundance of
neutrons
o responsible for the naturally occurring heavier elements
o Humans are made of stardust
o During a supernova explosion, its elements are dispersed throughout the universe which means that
its stardust eventually collects creating other heavenly bodies like earth
 Some of the material that makes us up is old as the universe itself

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Module 5: From Elements to Compounds
 focuses on interactions of elements that convert them into compounds.
 will discuss “why and how elements combine to form compounds”, with emphasis on the formation of water
from hydrogen and oxygen

 It is believed that comets and asteroids brought into the earth oceans worth of water (Fazekas, 2014), and
water would have been formed by the combination of oxygen produced by stellar nucleosynthesis and
hydrogen left over from the Big Bang (Hyman, n.d.).
 The intense heat from earth could also have combined the hydrogen and oxygen that were present on our
planet.
 the synthesis of water from its elements hydrogen and oxygen will be explained using modern atomic theory
and chemical bonding concepts. The molecular structure, polarity, and geometry of water will also be
discussed in connection with its physical properties of water that are important to its roles.

Learning Outcomes
At the end of this module, you should be able to:
1. Explain why and how elements combine to form compounds, with emphasis on why and how hydrogen and
oxygen combine to form water;
2. 2. Predict the geometry of water and other molecules using VSEPR theory;
3. 3. Discuss the factors that determine the physical properties of water; and
4. 4. Describe intermolecular and intramolecular forces in biological molecules.

5.1 Chemical Bonding Concepts: A Review

 Octet Rule: This is a chemical rule of thumb based on the observation that atoms of main-group elements
(representative elements) tend to combine in such a way that each atom has eight electrons in its valence
shell. This rule explains why atoms combine to form molecules and ions as a tendency for an atom to achieve
electronic stability like the inert gases — that is, to have eight electrons in its outermost shell (hydrogen is an
exception). The chemical reactivity and the bonds that hold atoms together in molecules and crystals are due
to the number of outer electrons (valence electrons) in any element.
 Periodic Properties: The present periodic table was constructed using atomic number as the basis of the
ordering of the elements. The order of the elements shows a periodic recurrence of properties of elements,
such that elements with similar properties are aligned in vertical columns. This is called “Periodic Law”. The
periodic recurrence of similar properties has been attributed to the periodic recurrence of similar electronic
configurations. These periodic properties are the following:
1. Atomic size - determined by the covalent radius (half the distance between the nuclei of identical atoms
when they are joined by a single covalent bond)
2. Ionization Energy (IE) or Ionization Potential - the minimum energy needed to remove the outermost
electron from the neutral atom in the gaseous state
3. Electron Affinity - the energy released when a neutral atom in the gaseous state accepts an electron in
its outermost shell to become a negatively charged ion (anion)
4. Electronegativity - the measure of the ability of an atom in a chemical compound to attract electrons
from another atom in a compound
5. Metallic Property - the tendency of an atom to lose electrons during chemical combination 6.
6. Nonmetallic Property - the tendency of an atom to gain electrons during chemical combination
 Chemical Bond: When the atoms of elements combine, chemical bonds are formed. Chemical bonding refers
to interactions that account for the association of atoms into molecules, ions, crystals, and other substances.
It is therefore, through chemical bonding that compounds are formed from elements.

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 Lewis Structure: A Lewis structure is a structural representation of a molecule where dots are used to show
the position of electrons around the atom(s) and lines or dot pairs are used to represent covalent bonds
between atoms. The types and ratio of atoms that combine, and how the atoms are connected to one
another in a molecule, and the nonbonding pairs of electrons, if present, can be deduced from the Lewis
structure.

 Types of Compounds
 Atoms of different elements behave differently when they interact with each other.
o Metals easily give away their valence electrons due to their low ionization energy, whereas the
nonmetals keep them due to high ionization energy.
 Thus, during combination, the metal transfers its valence electrons to the nonmetal, and because
atoms are electrically neutral, the metal, after giving away its valence electrons, becomes
positively charged, and the nonmetal, after accepting the electrons, becomes negatively charged.
o By electron transfer, both the metal and the nonmetal achieve electronic stability like the inert gases.
This is called ionic bonding, and the bond that holds the two oppositely charged ions is called an
ionic bond.
 Examples of ionic compounds are sodium chloride (NaCl, table salt) and ferric oxide (Fe2O3,
rust).
o On the other hand, atoms of nonmetals combine by sharing electrons.
 These atoms of high ionization energy and high electronegativity do not give away their
electrons.
 That is why during combination they simply share their valence electrons.
 The sharing generates a chemical bond called covalent bond, and the compound formed is called
a covalent compound or a molecular compound.
 Examples of covalent compounds are O2, H2O, glucose, and sucrose.

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5.2 Formation of Compounds

5.2.1 VSEPR Theory

 Molecules have shape. The primary reason why molecules assume a specific geometry is to be able to keep
the electron groups around the central atom as far apart as possible to prevent electrostatic repulsion.
 This is called valence shell electron pair repulsion (VSEPR) theory. Because electrons are negatively
charged, they should be most stable when they are far apart.
 In the Lewis structure of water, there are two bonding pairs and two lone pairs (Figure 2A). If these four pairs
of electrons are arranged as far apart as possible, we can predict the two pairs of bonding electrons and two
nonbonding lone-pair electrons to correspond to the corners of a tetrahedron. If the molecular geometry of
water is tetrahedral, the H-to-O-to-H bond angle in water will be 109.5 degrees. However, because electrons
are negatively charged, repulsion occurs between the two nonbonding pairs, between the bonding pairs, and
between the nonbonding and bonding pairs, which in turn causes the bond angle to be less than 109.5
degrees. Experiments indicate a value of approximately 104.48°. However, because the shape of a molecule
is described in terms of arrangement of atoms, not the electrons, the spatial arrangement of the two H-O
bonds in water will determine its shape. Hence, a water molecule is bent, not tetrahedral, as shown by
various spectroscopic methods and diffraction methods.
 How does the geometry of a water molecule determine its polarity?
 Generally, for a molecule to be polar it must have a polar bond.
o However, it should be noted that there are molecules with polar bonds that are not polar due to the
cancellation of bond dipoles.
 A molecule with two or more polar bonds must have asymmetric geometry so that the bond
dipoles will not cancel.
 On the other hand, a molecule is nonpolar when there is an equal sharing of electrons between
the two atoms of a diatomic molecule or because of the symmetrical arrangement of polar
bonds in a more complex molecule

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5.2 Structure and Properties of Water
 Water, the liquid of life, is considered one of the most important chemical compounds on earth.
 It covers about 70 % of earth’s surface. A human body is about 50-75 % water; the human brain is 75 %
water; and blood is 83 % water (Eubanks et al., 2008).
 Water is so important that we can survive for weeks without food but only days without water.
 Knowing the shape of a substance’s molecules is key to understanding its physical and chemical behavior.
 How does the polarity of water determine its properties?
 Water is polar due to the presence of partially positive hydrogen and partial negative charge of oxygen.
 When two water molecules approach each other, the partially positive-charged hydrogen atom of one
water molecule is attracted to the region of partial negative charge associated with the nonbonding
electron pairs on the oxygen of the other water molecule. This is called hydrogen bond.
 Hydrogen bond is a weak electrostatic attraction between a hydrogen atom bearing a partial positive
charge and an O atom bearing a partial negative charge (or nitrogen bearing partial negative charge).
o Hydrogen bonds are not shared electrons and are thus not covalent bonds.

 Although hydrogen bonds are not as strong as covalent bonds, the hundreds of thousands of hydrogen bonds
between the molecules of liquid water provide strong forces that keep the water molecules intact. These
strong intermolecular forces in liquid water explain several properties of water, such as its high boiling point
(100 °C) and high heat of vaporization (540 cal/g). When water boils, the water molecules are separated from
each other and moved into the gaseous state, where they are much farther apart. This happens when the
intermolecular hydrogen bonds are broken by heat. If the hydrogen bonds in water were weaker, water
would have a much lower boiling point and would require less energy to boil. Moreover, because evaporation
requires the separation of molecules, a greater amount of heat will be needed to break the strong
intermolecular forces between water molecules.
 When comparing two liquids, one consisting of polar molecules and the other nonpolar molecules, with
comparable molar masses, the liquid consisting of polar molecules boils at a higher temperature compared
to the other because the dipole–dipole interactions between polar molecules are stronger compared to the
London dispersion forces existing between nonpolar molecules. It should be noted, however, that London
forces can be stronger than dipole-dipole interactions depending on the surface area of the molecules.

5.3 Chemical Bonds (Intermolecular and Intramolecular Forces) in Biological Molecules

 Hydrogen bonds are very important intermolecular and intramolecular forces that determine the shape of
biomolecules with partially positive hydrogen and electronegative atom N or O
 These bonds are important in stabilizing the shape of large molecules, such as proteins and nucleic acids.
In proteins, which are the major component of skin, hair, and muscle, hydrogen bonding occurs between
the polar peptide bonds that join the amino acids.

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  These hydrogen bonds stabilize the secondary structures of proteins (Figure 4). In the beta-pleated sheet
(left picture), hydrogen bonds occur between the two parallel polypeptides (intermolecular); in the
alpha-helix (right side), hydrogen bonds are between the peptide bonds within the polypeptide chain
(intramolecular).

 In deoxyribonucleic acid (DNA), which contains the genetic information, the coiled double-helical
structure is stabilized by thousands of hydrogen bonds between adenine and thymine (two hydrogen
bonds) and guanine and cytosine (three hydrogen bonds)
 Some biomolecules interact by hydrophobic (nonpolar) interactions called London dispersion forces.
 The London dispersion force is the weakest intermolecular force since it is only a temporary attractive
force between nonpolar molecules.
 Its relative strength depends on the surface area of molecules interacting such that it is stronger for
molecules with a large surface area.
 The cell membranes of animal cells are composed mostly of phospholipids, molecules with long
hydrophobic tails (nonpolar tails).

o These hydrophobic tails of phospholipids interact via London forces, which in this case are strong
enough to make the membrane semi-fluid, a state important to its function of regulating the passage
of ions and molecules through it.
o The inner nonpolar part of the membrane allows the many nonpolar molecules to pass through it
while preventing the polar molecules and ions. In this way, the cell membrane is able to act as barrier
to the entry of molecules and ions into the cells and in leaving the cells.
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  In general, polar molecules have stronger intermolecular forces than nonpolar compounds. The more polar a
molecule is, the stronger is its intermolecular force.
 Hydrogen has unusually high bond strength when it is bonded with F, O, or N.

5 – PPT: From Elements to Compounds

Bonding
 Atoms with unfilled valence shells are considered unstable.
 Atoms will try to fill their outer shells by bonding with other atoms.
 Chemical bond = the attractive force that holds atoms or ions together in a
compound

Atomic Bonds
 Atoms form atomic bonds to become more stable.
 Atoms become more
stable by filling their
valence shell or at
least meeting the
octet rule by getting
8 valence electrons.
 Exception to octet
rule of 8 valence
electrons: Helium—
which only has 1
energy level and
holds a maximum of
2 electrons

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  There are three main types of chemical bonds used by atoms to fill their valence shell:
 Metallic

 Ionic

 Covalent

Metallic Bonds
 are metal to metal bonds formed by the attraction between positively charged
metal ions and the electrons around them.
 Atoms are packed tightly together to the point where outermost energy
levels overlap.
o This allows valence electrons to move freely from one atom to the next
making them great conductors of electricity.

Ionic Bonds
 are formed between metals and non-metals.
 are formed by the transfer of electrons.
 One atom loses (gives away) electrons.
 One atom gains (receives) electrons.

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Covalent Bonds
 bonds formed between two non-metals.
 are formed when atoms SHARE electrons.
 Both atoms need to gain electrons to become stable, so they share the electrons they have.
 Atoms can share more than one pair of electrons to create double and triple bonds.

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VSEPR Theory
 The basic principles of VSEPR Theory:
 Electron pairs repel each other.
 Electron pairs in molecules tend to arrange themselves so as to
minimize the repulsion between them.
 In other words, get as far apart as possible.
 Repulsion strength:
o lone pair-lone pair > lone pair-bond pair > bond pair-bond pair

Why the shape of a molecule is important

 The shape of a molecule may determine its properties and uses Why the shape of a molecule is important
 Properties such as smell, taste, and proper targeting (of drugs) are all possible because of the shapes of
molecules

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 In this geometry, there is only one molecular geometry
 NOTE: If there are only two atoms in the molecule, the molecule will be linear no matter what the geometry
is.

 There are two molecular geometries:

 Trigonal planar, if there are no lone pairs
 Bent, if there is a lone pair

 There are three molecular geometries:

 Tetrahedral, if no lone pairs
 Trigonal pyramidal if one is a lone pair
 Bent if there are two lone pairs

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 There are four distinct molecular geometries in this domain:
 Trigonal bipyramidal
 Seesaw
 T-shaped
 Linear

 All positions are equivalent in the octahedral domain.

 There are five molecular geometries:
 Octahedral
 Square pyramidal
 Square planar
 T-shaped
 Linear

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Types of covalent bonds
 Nonpolar covalent bond
 Electrons are shared equally in the bond

 Polar covalent bond

 Electrons unevenly shared
 Electronegativity difference greater than zero but less than 2.0
 Chlorine pulls harder on the shared electrons than hydrogen does.
 Therefore, the chlorine end has more electron density than the hydrogen end.

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Nonpolar Molecules
 Sometimes the bonds within a molecule are polar and yet the molecule is nonpolar
because its shape is symmetrical.
 The individual dipoles cancel such that the overall dipole moment = 0

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5 – V1 Water: A Polar Molecule (Bozeman Science)

What does it mean to be Polar?

 It has a charge as electrons are shared unequally.

 Oxygen pulls the electrons from hydrogen

 Water is always oriented in a way that the positive of the hydrogen and the negative of the oxygen are
attracted to each other.

Hydrogen Bonding
 Positive hydrogen to the negative oxygen

Properties of Water
1. Cohesion
2. Capillary Action
3. High Specific Heat
 You have to pull the molecules apart
 Evaporate – you have to free one molecule
 Temperature of Areas surrounded by water are moderated
o Water absorbs a lot of energy – moderating the temperature
4. Ice Floats
 Water cools down – forms matrix – decreased density, thus, does not sink
5. Good Solvent
 Being surrounded by the positive charges of oxygen – allows quick dissolution of materials
 Anything that has a charge, water can break down
o Exceptions are anything non-polar

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5 – V2 How polarity makes water strangely behave (Christina Kleinberg – TED-Ed)

Polarity
 Unequal sharing of electrons within a molecule

Bonds in the Water Molecule: Polar Covalent bonds

Properties:
1. Cohesion
 Ability to stick to itself
2. Adhesion
 Ability to stick to other substances
3. Surface Tension
 Thin film in the surface of water due to hydrogen bonding allows light insects to walk on water
o Thin film cannot hold humans though
4. Ice can float
 Hydrogen bonds keep water molecules further apart in frozen water
 The further apart, the denser it is

Water is unique because of its Polarity or it is a Polar Molecule

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Module 6: Self-Assembly
 400 BC: Democritus (Greek philosopher) - imagined that all matter in the universe evolved from the
organization of atomistic components to form the Earth and solar system, stars, and galaxies.
 2000 years late: Descartes (French Philosopher) - envisioned an ordered universe arising out of chaos
through the self-organization of small objects into larger assemblages.
 The ideas of Democritus and Descartes were considered to have inspired later theories of self-assembly in
physics and mathematics, biology, and chemistry (Russell, 1972 as cited in Ozin, et al., 2009).

 module provides an overview of self-assembly, a process that takes place at various scales, from the
microscopic to the cosmologic.
 At the microscopic scale, subatomic particles self-assemble to form atoms, atoms self-assemble to form
molecules, and molecules self-assemble to form crystals.
 At the cosmic scale, stars self-assemble to form galaxies and galaxies self-assemble to form galaxy
clusters (Reishus, 2009).

LOs
1. Explain self-assembly;
2. Differentiate the types of self-assembly; and
3. Discuss the importance of self-assembly.

6.1 What is Self-Assembly?

 Nature is very good at building incredible structures.
 it uses molecules like proteins and lipids for its building blocks.
 For instance, a seed can take the nutrients from the soil and water and rearrange them and grow into a
tree.
Self-assembly
 is a process where separate or distinct components form spontaneously (i.e. with no human intervention)
into well-defined aggregates
 The size of the components may vary from the microscopic to the macroscopic.
 The process produces stable aggregates and is reversible.
 The components either equilibrate between aggregated and non-aggregated states or adjust their
positions relative to each other once the aggregates are formed (Whitesides & Grzybowski, 2002).
 can occur at various levels, from molecules to galaxies, provided that suitable conditions are satisfied
 Complex biological supramolecules like proteins, lipid bilayers, DNA, and polysaccharides, and non-
biological superstructures such as liquid crystals, silicate minerals, and graphite are formed through self-
assembly
 The formation of bacterial colonies, schools of fish, weather patterns, planets, the solar system, and the
galaxies are examples of self-assembly (Whitesides & Grzybowski, 2002)
 accounts for the emergence of order from disorder and the emergence of life
 plays an important role in nanotechnology, and has various applications in manufacturing, robotics, netted
sensors, computer networks, and the like (Whitesides & Grzybowski, 2002).

6.1.1 Self-Assembly at All Scales (by Whiteside, G.M. and Gryzbowski, B.)
Self- assembly
 is the autonomous organization of components into patterns or structures without human intervention
 Self-assembling processes are common throughout nature and technology

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  involve components from the molecular (crystals) to the planetary (weather systems) scale and many
different kinds of interactions
 The concept of self-assembly is used increasingly in many disciplines, with a different flavor and emphasis in
each.

Reasons for Interest in Self-assembly

1. Humans are attracted by the appearance of order from disorder.
2. Living cells self-assemble, and understanding life will therefore require understanding self-assembly.
 The cell also offers countless examples of functional self-assembly that stimulate the design of non-living
systems.
3. Self-assembly is one of the few practical strategies for making ensembles of nanostructures.
 It will therefore be an essential part of nanotechnology.
4. Manufacturing and robotics will benefit from applications of self-assembly.
5. Self-assembly is common to many dynamic, multicomponent systems, from smart materials and self-healing
structures to netted sensors and computer networks.
6. The focus on spontaneous development of patterns bridges the study of distinct components and the study
of systems with many interacting components. It thereby connects reductionism to complexity and
emergence (3).

Is Anything Not Self-Assembly?

 Processes ranging from the non-covalent association of organic molecules in solution to the growth of
semiconductor quantum dots on solid substrates have been called self-assembly.
 Here, we limit the term to processes that involve pre-existing components (separate or distinct parts of a
disordered structure), are reversible, and can be controlled by proper design of the components.
 “Self-assembly” is thus not synonymous with “formation.”

Types of Self-Assembly
1. Static self-assembly (S)
 involves systems that are at global or local equilibrium and do not dissipate energy
o For example, molecular crystals (4, 5) are formed by static self-assembly; so are most folded, globular
proteins
 formation of the ordered structure may require energy (for example in the form of stirring), but once it is
formed, it is stable
 Most research in self-assembly has focused on this static type
2. Dynamic Self-Assembly (D)
 the interactions responsible for the formation of structures or patterns between components only occur
if the system is dissipating energy
 The patterns formed by competition between reaction and diffusion in oscillating chemical reactions (6,
7) are simple examples; biological cells are much more complex ones
 The study of dynamic self-assembly is in its infancy
3. Templated Self-Assembly (T)
 interactions between the components and regular features in their environment determine the
structures that form
o Crystallization on surfaces that determine the morphology of the crystal is one example (8, 9)
o crystallization of colloids in three-dimensional optical fields is another (10)
4. Biological Self-Assembly (B)
 is the variety and complexity of the functions that it produces.

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6.2 Types of Self-Assembly

Molecular Self-assembly
 when molecules spontaneously assemble into supramolecules, without external work
 involves non-covalent or weak covalent interactions, such as van der Waals forces, electrostatic and
hydrophobic interactions, and hydrogen and coordination bonds
 The structure of the molecules usually determines the structure of the assembled product
 self-assembly of larger components or macroscopic substances involves other kinds of interaction such as
gravitational attraction, external electromagnetic fields, and magnetic, capillary, and entropic interactions
(Whitesides & Grzybowski, 2002).

Energy is either required or released during the self-assembly process.

 This determines the type of self-assembly

Static self-assembly (S)

 Processes that require energy to form the ordered structure (for example in the form of stirring)
 Once it is formed, it is stable. The phospholipid bilayer which makes the membrane of cells is an example of a
static self-assembled supramolecule (Figure 1a). It has a double layer of phospholipids where the nonpolar
tails aggregate forming the hydrophobic core and the polar ends forming the hydrophilic headgroups. Liquid
crystals are also formed by static self-assembly (Figure 1c)

Dynamic self-assembly
 Those that dissipate energy to form the ordered structure
 An example of a dynamic self-assembled structure is a school of fish

Templated self-assembly
 The formation of granite, an igneous rock,

Biological
 the formation of bacterial colonies

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6.3 Present and Future Applications of Self-assembly
 The concepts and principles of self-assembly were first elucidated in the study of molecules.
 From there, the concepts and principles of self-assembly have been applied in the synthesis of structures
larger than molecules
 The design of systems of components with nano- to macroscale dimensions can be aided significantly by
using analogies with molecular self-assembly systems.
 Self-assembly plays a key role in nanoscience and nanotechnology and it offers a possible route to the
fabrication of threedimensional microstructures (Whitesides & Boncheva, 2002)
 Some applications of self-assembly:

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Summary
 Self-assembly is a process in which separate or distinct components form spontaneously from disordered
structures to well-defined aggregates.
 The concepts and principles of self-assembly were first elucidated in the study of molecules. But the
potential of self-assembly as a process of forming useful and interesting structures extends far beyond
molecules.
 There appears to be limitless opportunity for the development of self-assembly as an approach to the
manufacture of complex systems.
 It may be applied to the assembly of electrically or optically functional components.
 Furthermore, using biomimetic strategies to expand the horizons of self-assembly beyond static systems into
dynamic self-assembly could open broad potential in this field (Whitesides & Boncheva, 2002).

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