UNIT-V

CARBON CLUSTERS AND NANOSTRUCTURES.

Nature of carbon bond - New carbon structures. Carbon clusters: Discovery of C60-Alkali doped
C60 - Superconductivity in C60 - Larger and smaller fullerenes. Carbon nanotubes: Synthesis -
Single walled carbon nanotubes - Structure and characterization- Mechanism of formation -
Chemically modified carbon nanotubes - doping functionallizing nonaotubes -Application of
carbon nanotubes.

Nanowires Nanotechnology and nonodevices: DNA as nanomaterial, DNA-knots and junction,

DNA nanomechemical device designed by Seeman. Force measurements in simple protein
molecules and polymerase - DNA complexs. Molecular recognition and DNA based sensor.
Protein nano array, nano pipette, molecular diodes, self assembled nano transistors, nanoparticle
mediated transfection.

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Nature of Carbon Bond

As of 2015, over 10 million organic compounds consisting of some combination of

carbon and other elements have been documented, with new organic compounds being
conceived and synthesized every day. The ability of carbon atoms to form covalent bonds with
itself is the most unique of its bonding properties and it is called catenation. This ability of
carbon atoms to combine with other atoms, including itself, enables carbon to form long,
continuous chains, branches and loops consisting of carbon and hydrogen in hydrocarbons and
only carbon in carbon allotropes as shown in figure 1.

Figure 1 Some allotropes of carbon: a) diamond, b) graphite, c) lonsdaleite, d–f) fullerenes (C60,
C540, C70); g) amorphous carbon, h) carbon nanotube.
Interestingly, carbon allotropes span a wide range of physical properties. Diamond is
transparent, the ultimate abrasive, and can be an electrical insulator and thermal conductor.
Conversely, graphite is opaque, a very good lubricant, a good conductor of electricity, and a
thermal insulator. This is the main component of the "lead" in pencils. Allotropes of carbon are

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not limited to diamond and graphite, but also include buckyballs (fullerenes), amorphous carbon,
glassy carbon, carbon nanofoam, nanotubes, and others.
Carbon has an affinity for bonding with other small atoms, including other carbon atoms,
via the formation of stable, covalent bonds. In diamond, all the carbon atoms share one electron
with each of their four neighboring carbon atoms. In case of graphite, instead of each carbon
having four neighbours, it only has three. Each carbon shares one electron with two of its
neighbours, and 2 electrons with the third neighbor. In this way, one C-C bond out of three is a
double bond. The atoms all bond together in planes and the planes stack on top of each other.
The key to understanding the various structural, thermal, and electric properties of carbon
nanostructures is the carbon bond, which can be single, double, or triple bond order.

Despite the fact that it is present in a vast number of compounds, carbon is weakly
reactive compared to other elements under normal conditions. At
standard temperature and pressure, it resists oxidation; it does not react with sulfuric acid,
hydrochloric acid, chlorine, or any alkali metals. At higher temperatures, carbon will react
with oxygen to give carbon oxides, and metals to give metal carbides.

New Carbon Structure

Researchers from North Carolina State University have discovered a new phase of solid
carbon, called Q-carbon, which is distinct from the known phases of graphite and diamond. Q-
carbon exhibits a random amorphous structure that is a mix of 3-way (sp2) and 4-way (sp3)
bonding rather than the uniform sp3 bonds found in diamonds. The process for creating Q-carbon
starts with a substrate, such as such as sapphire, glass or a plastic polymer. The substrate is then
coated with amorphous carbon – elemental carbon that, unlike graphite or diamond, does not
have a regular, well-defined crystalline structure. The carbon is then hit with a single laser pulse
lasting approximately 200 nanoseconds. During this pulse, the temperature of the carbon is
raised to 4,000 Kelvin (or around 3,727 degrees Celsius) and then rapidly cooled. This operation
takes place at one atmosphere – the same pressure as the surrounding air. The end result is a film
of Q-carbon, and the process could be controlled to make films between 20 nanometers and 500
nanometers thick.

Q-carbon can be converted to make diamond-related structures at room temperature and

at ambient atmospheric pressure in air, by changing the rate of cooling. These diamond objects

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have a single-crystalline structure, making them stronger than polycrystalline materials. All these
operations can be done at room temperature and at ambient atmosphere. Q-carbon has some
unusual characteristics. It is ferromagnetic, which could not be found among other solid forms of
carbon. In addition, Q-carbon is harder than diamond and glows when exposed to even low
levels of energy. Due to Q-carbon’s strength and low work-function it releases electrons easily
which makes it very promising for developing new electronic display technologies.

Carbon Clusters

A cluster is a group of a small, often variable, number of interacting atoms, ions or

molecules. Due to the enormous bonding flexibility of carbon, viz. its unique ability to form
stable single, double, or triple bonds, carbon clusters appear in a wide range of structural forms
that are synthesized spontaneously in hot carbon plasmas produced during the energetic
processing of carbon-rich materials. The most widely used laboratory technique for producing
carbon clusters has been laser vaporization of graphite followed by supersonic expansion into an
inert carrier gas, usually He or Ar. Neutral, anionic, and cationic carbon clusters form directly
from the laser initiated plasma in sizes ranging from one to hundreds of atoms. Carbon cluster
structure ranges from linear chains to rings to closed spheroidal cages to nanotubes.

Other methods of producing carbon clusters that do not involve laser vaporization include
the carbon are synthesis of macroscopic quantities of fullerenes and nanotubes, electric
discharge, photolysis, or pyrolysis of small hydrocarbon precursors, CO2 laser vibrational
activation of SF6 in the presence of acetylene, and Cs ion sputtering of graphite. Diederich and
coworkers and others have been developing techniques to systematically synthesize specific
sized carbon clusters from organic precursors. They have shown, for example, that C18 can be
produced by photolyzing an 18-membered cyclic carbon ring stabilized by organic leaving
groups.

Discovery of C60

For centuries it was believed that the element carbon only existed in 2 very different
forms, soft, black, conductive graphite and hard, transparent, insulating diamond. However in
1985 a new form of carbon was discovered, which had a remarkable structure. This form of

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carbon was composed of hexagons and pentagons of carbon, joined together to form a
completely spherical shape of a football! (Figure 2).

Figure 2 Structure of C60

The story began back in the early 1970's, when the chemistry of unsaturated carbon-
based molecules was being studied by a group at the University of Sussex, led by Richard E.
Smalley, Robert F. Curl, and Harold W. Kroto. They developed methods for synthesizing long-

chain polynes (compounds with many triply-bonded carbons, ( ), and

long-chained polynyl cyanides, HC5N, HC7N and HC9N (for e.g. )

These molecules were of interest because they are produced by red giant stars and had
been detected by radio astronomy in the cloud material of the interstellar medium. The carbon
plasma produced by the laser vaporization was probed by time-of-flight mass spectrometry. The
experiments confirmed that large carbon chain/clusters were being formed. But during the
experiments it was noted that the peaks for mass 720 (corresponding to 60 carbon atoms) and to
a lesser extent, for 840 (corresponding to 70 carbons), behaved unusually and formed under all
conditions as well as exhibiting great stability.

This experimental evidence indicated that a carbon molecule with sixty carbon atoms was
forming, but provided little structural information. The research group concluded after reactivity
experiments, that the most likely structure was a spheroidal molecule. But it wasn't known
exactly how 60 carbons could arrange themselves to form a sphere. But then Kroto recalled
seeing the geodesic dome structure at the centre piece of the Expo 67 exhibition in Montreal,

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which was a closed hemispherical shape containing linked pentagons as well as hexagons. He
realized that this was the way the carbons were arranged in C60, and so the molecule was named
after the architect of the geodesic structure, Buckminster Fuller. C60 itself, is therefore known as
Buckminster Fullerene, or 'Bucky balls' for short. Other similar closed cage structures, such as
the oval C70, were quickly discovered, and the entire family of such cages was called the
'fullerenes'

Alkalli Doped C60

Since the discovery of the carbon nanotube, 1D nanometer-scale materials have become
the focus of intense research owing to their unique structures and physical properties. Because
fullerenes are the most important novel materials in the carbon family, by using C60 as building
block, 1D C60 materials, such as C60 nanorod, nanotube and nanowire, have been synthesized and
especially attracted much attention in recent years. Alkali metal doped fullerides AxC60, where,
A is an alkali metal (Li, Na, K, Rb and Cs) and x is the stoichiometry of the composition, are
particularly interesting since their electronic properties are strongly related to the size of the
intercalated metal and the doping concentration (Figure 3). They can exhibit semiconducting,
metallic, or even superconducting properties. In general, alkali metal doped C60 have been
synthesized mainly by two methods, i.e., solid–solid reaction and vapour evaporation.

Figure 3 A schematic model of C60 fullerene balls in a regular lattice with alkali atoms
occupying the interstitial spaces.
Alkali doped C60 fullerene could be prepared as detailed below. A Muffle furnace was
used for our doping alkali on C60. Which enables to reach temperature up to several hundred
degree. A known amount of C60 nanotubes grown on glass substrate and an excess amount of Li,
Na and K metals were inserted at the two ends of a sealed, evacuated Pyrex tube under N2 gas
atmosphere, which was then kept at 200oC for 24 hours. A small temperature gradient in the

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furnace kept the alkali metals from condensing on the fullerene powder. The temperature used
for the synthesis of Li6C60, Na6C60, K6C60, Rb6C60 and Cs6C60 are 200oC. Various temperatures
on the doping concentration for alkali metals were expanded to the range from 150oC -295oC,
with intervals of about 50oC for each step, at 150oC, 200oC, 250oC and 295oC, respectively. The
doping concentration of Li and Na changed from low to high level, depending on the experiment
temperatures and alkali metals, and the high level doping can be obtained above the critical
temperatures and the K doping was always saturated (K6C60). The samples were then slowly
cooled down to room temperature for further Raman spectroscopy characterization using
excitation wavelengths of 514.5 nm (Ar+) at room temperature.

Superconductivity of C60

The interaction of alkali-metal atoms in solid C60 leads to metallic behavior and it show
superconductivity. It was found by Haddon and co workers in 1991. The alkali metal like
potassium-doped C60 becomes superconducting at 18 K. This was the highest transition
temperature for a molecular superconductor. Since then, superconductivity has been reported in
fullerene doped with various other alkali metals 29 K (Rb3C60), and 33 K for (RbCs2C60) are
lower than those of the cuprates, MgB2, and the Fe-pnictide. It has been shown that the
superconducting transition temperature in alkaline-metal-doped fullerene increases with the unit-
cell volume V. As caesium forms the largest alkali ion, caesium-doped fullerene is an important
material in this family.
The C60 molecules compose a solid of weakly bound molecules. The fullerites are
therefore molecular solids, in which the molecular properties still survive. The discrete levels of
a free C60 molecule are only weakly broadened in the solid, which leads to a set of essentially
non overlapping bands with a narrow width of about 0.5 eV. For an undoped C60 solid, the 5-fold
hu band is the HOMO level, and the 3-fold t1u band is the empty LUMO level, and this system is
a band insulator. But when the C60 solid is doped with metal atoms, the metal atoms give
electrons to the t1u band or the upper 3-fold t1g band. This partial electron occupation of the band
may lead to metallic behavior. However, A4C60 is an insulator, although the t 1u band is only
partially filled and it should be a metal according to band theory. This unpredicted behavior may
be explained by the Jahn–Teller effect, where spontaneous deformations of high-symmetry
molecules induce the splitting of degenerate levels to gain the electronic energy. The Jahn–Teller

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type electron-phonon interaction is strong enough in C60 solids to destroy the band picture for
particular valence states.
Larger and Smaller Fullerenes

Larger fullerenes such as C70, C76, C80 and C84 and even up to 100 carbon atoms are
commonly obtained (Figure 4). The smallest fullerene is the dodecahedral C20. There are no
fullerenes with 22 vertices. The number of fullerenes C2n grows with increasing n = 12, 13, 14,
roughly in proportion to n9. For instance, there are 1812 non-isomorphic fullerenes C60.

Figure 4 Structures of Larger and Smaller Fullerenes

Note that only one form of C60, the buckminsterfullerene alias truncated icosahedron, has
no pair of adjacent pentagons (the smallest such fullerene). However, the high curvature of
C20 and other smaller structure carbon atoms is too unsuitable for sp2-hybrid state of carbon,
which prefers flat coordination. Therefore, the smallest stable pristine fullerene is C60, a
truncated icosahedron where all pentagonal faces are separated from each other by hexagonal
ones. This fact is a manifestation of the isolated pentagon rule (IPR), well-known in fullerene
chemistry, obeyed by all pristine fullerenes available in reasonable quantities. Because of the
IPR, C60 fullerene is followed by C70 since there are no intermediate structures with isolated
pentagons. Beyond C70, there exist fullerenes with any even number of carbon atoms, so-called
higher fullerenes. Furthermore, starting with C78, several stable isomers are observed for each
carbon skeleton.

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 A C20 dodecahedral carbon molecule has been synthesized by gas phase dissociation of
C20 HBr13. C36H4 has also been made by pulsed laser ablation of graphite. A solid phase of C22
has been identified in which the lattice consists of C20 molecular bonded together by an
intermediate carbon atom. One interesting aspect of the existence of these smaller fullerenes is
the prediction that they could be super conductors at temperatures when appropriately doped.

Carbon Nanotubes

A carbon nanotube (CNT) or molecular tubes is allotropes of carbon with a cylindrical

nanostructure, having a diameter measuring on the nanometer scale (Figure 5). They have
incredible properties, which are valuable for nanotechnology, electronics, optics and other fields
of materials science and technology. A nanometer is one-billionth of a meter, or about 10,000
times smaller than a human hair. CNT are unique because the bonding between the atoms is very
strong and the tubes can have extreme aspect ratios.

Figure 5 Structure of single-walled nanotubes (A) and multi-walled nanotubes (B).

CNT are members of the fullerene structural family. Their name is derived from their
long, hollow structure with the walls formed by one-atom-thick sheets of carbon, called
graphene. These sheets are rolled at specific and discrete (Chiral) angles and the combination of
the rolling angle and radius decides the nanotube properties; for example, whether the individual
nanotube shell is a metal or semiconductor. Figure shown above represents two different type of
nanotubes namely, single-walled nanotubes (SWNTs) and multi-walled nanotubes (MWNTs).
Individual nanotubes naturally align themselves into "ropes" held together by Van der Waals
forces, more specifically, pi-stacking.

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Synthesis Carbon Nanotubes
Historically, the oldest method for the carbon nanotube production is the electric arc
discharge. Other methods such as the laser evaporation/ablation and chemical vapour deposition
(CVD) were also successfully examined. The laser evaporation process is technically similar to
the arc discharge method. The difference between these two methods is in the quality and purity
of the obtained products.
i) Arc discharge technique.
The arc discharge technique (Figure 6) generally involves the use of two high-purity graphite
electrodes. The anode is either pure graphite or contains metals. In the latter case, the metals are
mixed with the graphite powder and introduced in a hole made in the anode center. The
electrodes are momentarily brought into contact and an arc is struck.

Figure 6 Schematic representation of arc discharge apparatus for the synthesis of CNT.
The synthesis is carried out at low pressure (30-130 torr or 500 torr) in controlled atmosphere
composed of inert reactant gas. The distance between the electrodes is reduced until the flowing
of a current (50–150 A). The temperature in the inter-electrode zone is so high that carbon
sublimes from the positive electrode (anode) that is consumed. A constant gap between the
anode and cathode is maintained by adjusting the position of the anode. Plasma is formed
between the electrodes. The plasma can be stabilized for a long reaction time by controlling the
distance between the electrodes by means of the voltage (25–40 V) control. The reaction time
varies from 30–60 seconds to 2–10 minutes. Various kinds of products are formed in different
parts of the reactor: (1) large quantities of rubbery soot on the reactor walls; (2) web-like

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structures between the cathode and the chamber walls; (3) grey hard deposit at the end of
cathode; and (4) spongy collaret around the cathodic deposit. The metals usually utilized were
Fe, Ni, Co, Mo, Y either alone or in mixture. Better results were obtained using bimetallic
catalysts. Amorphous carbon, encapsulated metal nanoparticles, polyhedral carbon are also
present in the product.

MWNTs together with graphite carbon nanoparticles are found in the carbon deposit. The
inner diameter of the MWNTs varies from 1 to 3 nm, the outer diameter varies in the range of 2–25
nm, the tube length does not exceed 1 μm, and the tubes have closed tips. When metal catalysts are
co-evaporated with carbon in the DC arc discharge, the core of the deposit contains MWNTs, metal
filled MWNTs (FMWNTs), graphitic carbon nanoparticles (GNP), metal filled graphite carbon
nanoparticles (FGNP) and metal nanoparticles (MNP), while the powder-like or spongy soot contains
MWNTs, FMWNTs and SWNTs. The SWNTs have closed tips, are free of catalyst and are either
isolated or in bundles. Most of the SWNTs have diameters of 1.1–1.4 nm and are several microns
long. The collarette is mainly constituted of SWNTs (80%), isolated or in bundles, but it is only
formed in the presence of certain catalysts.

ii) Chemical Vapour Deposition Method

A class of processes that seems to offer the best chance to obtain a controllable process for
the selective production of nanotubes with predefined properties is chemical vapour deposition
(CVD). The catalytic chemical vapour deposition (CCVD) method is considered as the only
economically viable process for large-scale CNT production and the integration of CNTs.

Figure 7 Schematic representation of arc discharge technique Used in synthesis of CNT

In principle, chemical vapour deposition is the catalytic decomposition of hydrocarbon or
carbon monoxide feedstock with the aid of supported transition metal catalysts. There are two

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types of furnace modality, one is a horizontal configuration, and the second is a vertical
configuration (Figure 7). The application of horizontal furnace is the most popular. Here the
catalyst is placed in a ceramic or quartz boat which is put into a quartz tube. The reaction
mixture containing a source of hydrocarbon and an inert gas is passed over the catalyst bed at
temperatures ranging from 500 °C to 1100 °C. The system is then cooled down to room
temperature. The vertical furnace configuration is usually employed for the continuous mass
production of carbon fibers/nanotubes.

The general nanotube growth mechanism in the CVD process involves the dissociation of
hydrocarbon molecules catalyzed by the transition metal, and the saturation of carbon atoms in
the metal nanoparticle. The precipitation of carbon from the metal particle leads to the formation
of tubular carbon solids in a sp2 structure. The characteristics of the carbon nanotubes produced
by CVD method depend on the working conditions such as the temperature and the operation
pressure, the kind, volume and concentration of hydrocarbon, the nature, size and the
pretreatment of metallic catalyst, the nature of the support and the reaction time. By varying the
active particles on the surface of the catalyst, the nanotube diameter can be controlled. The
length of the tubes depends on the reaction time; even up to 60 mm long tubes can be produced.

Sigel Walled Carbon Nanotubes (SWNTs)

Single-walled nanotubes (SWNT) have a diameter of close to 1 nanometer, with a tube
length that can be many millions of times longer. The structure of a SWNT can be
conceptualized by wrapping a one-atom-thick layer of graphite called graphene into a seamless
cylinder. Single-walled nanotubes are an important variety of carbon nanotube because they
exhibit electric properties that are not shared by the multi-walled carbon nanotube (MWNT)
variants.
In particular, their band gap can vary from zero to about 2 eV and their electrical
conductivity can show metallic or semiconducting behavior, whereas MWNTs are zero-gap
metals. Single-walled nanotubes are the most likely candidate for miniaturizing electronics
beyond the micro electromechanical scale currently used in electronics. The most basic building
block of these systems is the electric wire, and SWNTs can be excellent conductors. The
remarkable electrical properties of SWNTs stem from the unusual electronic structure of the two-
dimensional material, graphene, from which they are constructed.

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Structure and Characterization of SWNTs

A SWCNT can be viewed as a graphene sheet rolled into a cylinder which is terminated
by two half-fullerene caps. The diameter of these species typically ranges from 0.7 to 2.5 nm,
and their aspect ratio can be as high as 104–105. These very strong confinements along their
circumference make them behave like 1-D materials (Figure 8). To know about the crystal
structure of a SWCNT, it is important to first consider its parent material, graphene. Graphene is
a monolayer of sp2-hybridized carbon atoms arranged in a honeycomb lattice. Its unit cell is
defined by the primitive vectors a1 and a2. Each SWCNT is then indicated by a chiral vector Ch,
which specifies the two atoms of the graphene sheet which are identified upon formation of the
tube. The chiral vector is defined with respect to the graphene primitive vectors as,
Ch " na1+ma2 " (n, m)

Figure 8 (a) The unrolled hexagonal lattice of a nanotube. When we connect sites O–A, and B–
B', a nanotube can be constructed. OA and OB define the chiral vector Ch and the translational
vector T of the nanotube, respectively The rectangle OAB'B defines the unit cell for the
nanotube. The vector R denotes a symmetry vector.

Where, n and m are integers such that 0 ≤ m ≤ n. When we express the chiral vector Ch
in the form (n,m), we call it the chiral index. These two terms should be regarded as
synonymous. The angle θ formed between Ch and a1 is a quantity of great importance for
determining the electronic properties of the SWCNT; it is called the chiral angle, and is defined
through

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 The nanotube diameter can be computed from the chiral vector by,

Where, a C−C ≈1.44Å is the nearest neighbor distance between carbon atoms in graphene.
SWCNTs can be classified into threemain types:

1. Armchair nanotubes for which n ≠ m (i. e. Ch = (n, n))

2. Zig-zag nanotubes for which m ≠ 0 (i.e. Ch = (n, 0))
3. Chiral nanotubes (n &= m & ≠ 0) whose mirror images have a different structure and display
different properties for example in circular dichroism.

Figure 8 (b) The hexagonal lattice of all possible (n,m) species formed by rolling the (0, 0) point
onto (n,m). The empty circles are semiconducting (n,m), (# = ±1). The filled circles represent
metallic, # = 0 (n,m) species.

Armchair and zigzag nanotubes (having the highest symmetry) (Figure 8) are named after
the shape of their cross section along Ch. All three of these different structures will display
various physical properties and their distinction will be of prime importance for their electronic
structure, phonon dispersion and optical properties.
Characterization:
X-ray photoelectron spectroscopy (XPS) allows determining the functionalization of the
nanotubes. Binding energy and FWHM are modified in a significant way. New peaks appears
according to the bonds formed between carbon atoms and compounds added. Scanning tunneling
microscopy (STM) is a powerful technique used to obtain three-dimensional images and
electronic states of the nanotubes. Nanotubes helicities could be determined with high resolu-

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tion images. The features of the nanotubes are explored at a larger scale using neutron
diffraction. This diffraction technique allows investigating a large range of scattering vector
Q compared to X-ray diffraction. Thus, with a statistical approach, XRD is used to obtain some
information on the inter-layer spacing, the structural strain and the impurities. Numerous features
such as intershell spacing, chiral indices, and helicity are also obtained by transmission electron
microscopy (TEM). Infrared spectroscopy is often used to determine impurities remaining from
synthesis or molecules capped on the nanotube surface. But the most powerful technique to
characterize nanotubes remains the Raman spectroscopy: without sample preparation, a fast and
non-destructive analysis is possible. Moreover, Raman spectra simulations are performed on
various nanotubes geometries. For a correct characterization of nanotubes, all these techniques
described here cannot be used separately but must be used in complementary ways.
Mechanism of formation

A hydrocarbon vapor when comes in contact with the “hot” metal nanoparticles, first
decomposes into carbon and hydrogen species; hydrogen flies away and carbon gets dissolved
into the metal. After reaching the carbon-solubility limit in the metal at that temperature, as
dissolved carbon precipitates out and crystallizes in the form of a cylindrical network having no
dangling bonds and hence energetically stable. Hydrocarbon decomposition (being an
exothermic process) releases some heat to the metal’s exposed zone, while carbon crystallization
(being an endothermic process) absorbs some heat from the metal’s precipitation zone.

Figure 9 Widely accepted growth mechanism for CNTs. (A)- tip growth model and (B)-base
growth model.

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 When the catalyst-substrate interaction is weak, hydrocarbon decomposes on the top
surface of the metal, carbon diffuses down through the metal, and CNT precipitates out across
the metal bottom, pushing the whole metal particle off the substrate (Figure 9). As long as the
metal’s top is open for fresh hydrocarbon decomposition, the concentration gradient exists in
Carbon Nanotubes - Synthesis, (Figure 9, A-ii). Once the metal is fully covered with excess
carbon, its catalytic activity ceases and the CNT growth is stopped (Figure 9, A-iii). This is
known as “tip-growth model”. In the other case, (Figure 9, B), when the catalyst-substrate
interaction is strong (metal has an obtuse contact angle with the substrate), initial hydrocarbon
decomposition and carbon diffusion take place similar to that in the tip-growth case, but the CNT
precipitation fails to push the metal particle up; so the precipitation is compelled to emerge out
from the metal’s CNT growth mechanism. We are not sure that, during the CNT growth, whether
the metal is in solid or liquid state.

Chemically Modified Carbon Nanotubes

Doping
The unique morphology of nanotubes means that there are a wide variety of possible
approaches to dope them and thereby change their physical and electronic properties. Different
approaches to chemical functionalisation of nanotubes are shown in the figure 10.

Figure 10 Different approaches to chemical modification of carbon nanotubes. (a) Substitutional

doped single-walled nanotubes (b, c) Nanotubes bundles intercalated with atoms or ions, (d, e)
Peapods: SWNTs filled with fullerenes (other endohedral fillings are possible), (f) Fluorinated
tubes, (g) Covalently functionalized tubes and (h) functionalized nanotubes vai π-stacking of the
functionality and the tube.

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 Many of these take advantage of the molecular nature of the nanotubes, however it is also
possible to dope in the more traditional semiconductor industry sense, i.e. deliberately replacing
carbon atoms with impurities such as nitrogen to get nitrogen doped nanotubes. The possibility
of attaching functional groups to the nanotube surface allows the combination of the properties
of the nanotubes and the group attached to the CNT.

Functionalized Carbon Nanotubes

The chemical modification or functionalization of a carbon substrate material was first

reported by Murray et. al. in 1970s. CNTs can undergo chemical functionalization to enhance
solubility in various solvents and to produce novel hybrid materials potentially suitable for
applications (Figure 11). The main approaches for the functionalization of CNTs can be grouped
into two main categories: (a) the covalent attachment of chemical groups, through reactions on
the conjugated skeleton of CNTs, and (b) the non-covalent supramolecular adsorption or
wrapping of various functional molecules onto the tubes. The covalent functionalization of CNTs
allows functional groups to be attached to tube ends or sidewalls. The sites of highest chemical
reactivity in the CNT structure are the caps, which have a semi-fullerene like structure. Chemical
functionalization of CNT tips has been performed mainly on the basis of oxidative treatments.
As a general rule, CNT oxidation yields opened tubes with oxygen-containing functional groups
(predominantly carboxylic acid) at both the sidewall and the tube endings. These groups can then
be used as chemical anchors for further derivatization.
Functionalization of carbon nanotubes

Covalent functionalization
Disruption of graphitic skeleton
Loss of electronic properties
Stable bond formation Non-Covalent functionalization
Structuer and electronic network
retain unaffected
Sidewall
End-tip
Cycloaddition Van der Waals interactions Wrapping
Radical addition of polynuclear molecules Endohedral
Oxidation filling Decorration with nanoparticle
Esterification
Amidation
Figure 11 Overview scheme of the functionalization of carbon nanotubes.

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 Although the bonding in CNTs is similar to that of graphene, curvature of the nanotube
sidewall renders addition reactions to the cylindrical nanostructure more favorable than in a flat
graphene sheet. In addition, several experimental studies exist, which reveal that the exohedral
chemical reactivity increases with increasing curvature of the sidewall. This dependency has
been attributed to curvature induced strain that originates from pyramidalization of the sp 2-
hybridized carbon atoms and the misalignment of π-orbitals.
Another parameter that profoundly alters the chemical reactivity of CNT sidewalls is the
presence of defects. It has been estimated that approximately 2% of the carbon atoms in
SWCNTs occur in nonhexagonal rings. The presence of sidewall defects such as vacancies or
pentagon-heptagon pairs (Stone-Wales defects) results in a locally enhanced chemical reactivity
of the graphitic nanostructures. Apparently, covalent sidewall functionalization generates sp3
carbon sites on CNTs, which disrupt the band-to-band transitions of π electrons, and cause loss
of the novel properties of CNTs, such as their high conductivity and remarkable mechanical
properties. With increasing functionalization degree, the tubes can eventually convert into
insulating material. Partial restoring of the structural integrity of the starting material can be
accomplished by thermal annealing of the modified tubes at temperatures between 300 and 500
°C. The modification protocol was generally achieved by attaching specific molecule or entity
which imparts chemical specificity to the substrate material. Some examples of synthesis of
modified carbon nanotubes are described below (Figure 12-13).

Figure 12 Functionalization of nanotubes through amidation.

For example, in the amidation with the same amino-containing functional group (Figure-
12), the acyl chloride route generally produces samples that are more soluble than those from the
diimide-activated coupling reaction. The latter typically contain more bundled carbon nanotubes

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in the soluble fraction, so that the resulting solution exhibits a higher level of light scattering.
The degree of dispersion for the solubilized carbon nanotubes in solution can, in some cases,
affect significantly the observed properties of the nanotubes, such as their Raman and
luminescence properties.
Example-2

The metal oxides can be attached to the carboxyl groups without any linker due to their
hydrophilic nature as recently demonstrated for MnO2, MgO, TiO2 and Zr(SO4)2. It make weak
interactions between the oxides and the acid-terminated nanotubes resulting in rather nonuniform
distributions of the NPs.

Figure 13 Modification of CNTs with TiO2 and SiO2 nanoparticles via silane and phoephoric
acid bonds.

Better adhesion was observed when capping agents were used. Sainsbury and
Fitzmaurice produced capped TiO2 and SiO2 nanoparticles (d ≈4-5 nm) via a standard sol-gel
process using titanium tetraisopropoxide (TTIP) and tetraethyl orthosilicate (TEOS) as
precursors with cetyltrimethyl ammonium bromide (CTAB) as the capping agent.

Application of Carbon Nanotubes

Potential applications of carbon nanotubes are: (1) additives in polymers; (2) catalysts;
(3) electron field emitters for cathode ray lighting elements; (4) flat panel display; (5) gas-
discharge tubes in telecom networks; (6) electromagnetic-wave absorption and shielding; (7)

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energy conversion; (8) lithium-battery anodes; (9) hydrogen storage; (10) nanotube composites
(by filling or coating); (11) nanoprobes for STM, AFM, and EFM tips; (12) nanolithography;
(13) nanoelectrodes; (14) drug delivery; (15) sensors; (16) reinforcements in composites; (17)
supercapacitor.
Nanowire Nanotechnology and Nanodevices

DNA as a Nanomaterial

It is well known that the nucleotide sequence of DNA (deoxyribonucleic acid) molecules
is the blueprint of life and it is recognized as a nanomaterial, not as a biological material, in the
research field of nanotechnology. DNA is a macromolecule consisting of four types of
deoxyribonucleotides, termed deoxyadenylate (A), deoxythymidylate (T), deoxycytidylate (C)
and deoxyguanosinylate (G), linked together via phosphodiester bonds (Figure-14).

Figure 14 Double helix structure of DNA

Single-stranded DNA molecules with complementary sequences form a double helix via
the Watson–Crick base pairing scheme (A-T and C-G pairing). Aside from their role in biology,
DNA molecule exhibits intriguing properties, such as insulator, a good conductor, or a

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semiconductor with a large band gap, vast information storage, self-organisation and
programmability, making it an ideal material in the construction of nanodevices, nanoelectronics
and molecular computing.

DNA molecule is an insulated wire at low bias. Hence, making DNA conductive is
essential for the application of DNA in nanoelectronics. DNA has already been exploited for the
fabrication of nanoscaled systems. Convenient programming of nucleotide sequences and the
mechanical rigidity of short double helices of DNA molecules make DNA highly favourable for
the construction of nanodevices with designated 1D, 2D or 3D structures. Moreover, DNA
molecules can be easily engineered with atomic precision using DNA manipulating enzymes,
such as ligases, nucleases and transferases. DNA origami, a nano-scaled folding of single-
stranded DNA via interaction with a large number of short DNA oligonucleotides, to form
predefined 2D or 3D DNA structures at the nanoscale.
The introduction of metallic complexes (doping) onto both DNA (M-DNA) terminals to
act as both electron donors and electron acceptors. It has been considered as nanowire with
attractive conductivity and proved as a memristor system. The possibilities of merging the gap
between nano and macro devices may be achieved with M-DNA devices (Figure 15).

Figure 15 Conductive DNA nanowire (a) DNA only and (b) DNA with metals.
Metal ions were shown to bind strongly to the base pairs of DNA and are enclosed by the
phosphate sugar backbones. In a metal-doped duplex DNA complex, the hydrogen bonds
between complementary bases were replaced with metal ions. The duplex DNA can be doped
with divalent metal ions at pH ≥ 8.5 by substituting the imino proton of the base in the base
pairing. Interestingly, DNA possessed unusual conducting property when it was doped with Co 2+
or Ni2+ ions. By contrast, DNA may be mechanically deformed by doping with silver ions.

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DNA Knots and Junctions
DNA Knots
DNA packing can be visualized as two very long strands that have been intertwined
millions of times, tied into knots, and subjected to successive coiling. However, replication and
transcription are much easier to accomplish if the DNA is neatly arranged rather than tangled up
in knots.
DNA can be visualized as a complicated knot that must be unknotted by enzymes in
order for replication or transcription to occur. Enzymes act to slice through individual knots and
reconnect strands in a more orderly way. It is perhaps not surprising then that connections
between mathematical knot theory and biology have been discovered (Figure 16). By thinking of
DNA as a knot, we can use knot theory to estimate how hard DNA is to unknot. This can help us
estimate properties of the enzymes that unknot DNA. A mathematical knot is a closed curve.
This can be visualized as a closed loop of string. If the string had a knot in it, it would be
impossible to unknot without slicing throught the knot. Look at the pictures below.

Figure 16 Pictorial representation of DNA Knots

The first knot is merely a loop of string that has been twisted, an "unknot". It could easily
be unknotted by pulling on the string to form a single loop. The 2 nd knot, however, is clearly a
knot. The only way to get rid of the knot would be to cut through it and retie the string. The 3 rd
knot is even more complicated. To understand this more rigorously, we will explore some
topological definitions. A knot is a closed curve in three-dimensional space. Two knots are
considered the same if one can be moved smoothly through space, without any cutting, so that it

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is identical to the second. Mathematical knots are represented by two-dimensional diagrams that
can be thought of as the shadow cast by a three-dimensional knot.

At points in the diagram shown below, the curve will cross over or under itself. The
crossing points are called double points. Each double point is assigned a (+) or (-) sign,
depending on the orientation of the crossing point. If the strand passing over a double point can
be turned clockwise less than 180 to match the direction of the strand underneath, then the sign is
positive (+); if the strand on top must be rotated counter-clockwise, it is negative (-). The writhe
of a knot is the sum of all signs of its double points. The knots below are +3 and -3, respectively.

A knot is in its ideal form if it has been moved smoothly through space so that all excess
double points are removed. Knots are generally described by two numbers, C U, the ideal crossing
number (C) and the unknotting number (U). In the figure above, the knots would be 0 0 and 31,
respectively. Mathematical knots may have values for writhe and crossing number that are much
higher than the ideal number if they have been moved smoothly through space to a more
complicated form.

DNA Junctions

A Holliday junction is a branched nucleic acid structure that contains four double
stranded anti-parallel stacked-X form joined together. These arms may adopt one of several
conformations depending on buffer salt concentrations and the sequence of nucleo-bases closest
to the junction (Figure 17). The geometry of junctions had previously been described in terms of
a specific set of parameters that include: (i) the angle relating the ends of DNA duplexes arms of
the junction (inter duplex angle); (ii) the relative rotation of the duplexes about the helix axes of
the stacked duplex arms (Jroll); and (iii) the translation of the duplexes along these helix axes
(Jslide).The structure is named after the molecular biologist Robin Holliday, who proposed its
existence in 1964.
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Figure 17 Geometry of Holliday junctions. The junction formed by four strands of DNA
(labeled A, B, C and D, and colored blue, yellow, red and green, respectively) is characterized as
having four duplex arms extending from a junction center (left). The junction can form an
approximate square planar geometry (open-X form, center) when in low salt solutions or when
bound to proteins such as cre [light gray], or the more compact stacked-X structure (right) in
which the arms form stacked pairs. This latter stacked-X structure is shown here with the A-arm
stacked on D, and the B arm stacked on C to give two sets of nearly continuous B-DNA type
helices.

In biology, Holliday junctions are a key intermediate in many types of genetic

recombination, as well as in double-strand break repair. These junctions usually have a
symmetrical sequence and are thus mobile, meaning that the four individual arms may slide
through the junction in a specific pattern that largely preserves base pairing. Additionally, four-
arm junctions similar to Holliday junctions appear in some functional RNA molecules. Immobile
Holliday junctions, with asymmetrical sequences that lock the strands in a specific position, were
artificially created by scientists to study their structure as a model for natural Holliday junctions.
These junctions also later found use as basic structural building blocks in DNA nanotechnology,
where multiple Holliday junctions can be combined into specific designed geometries that
provide molecules with a high degree of structural rigidity.

In solution, the two forms of the Holliday junction that have been observed are the open-
X form, which is favored in low-salt conditions, and the stacked-X form, which is observed

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under physiological concentrations of mono- and multivalent cations. The stacked-X structure is
characterized by having the arms paired to form nearly continuous B-DNA duplexes, interrupted
only at the junction crossovers. The arms can undergo a conformational isomerization where the
stacked duplexes can switch partners dynamically (12±14), and apparently involves unstacking
of the duplex arms into the open-X conformation. The transition from the stacked-X to open-X
structure also provides a means for the junction to freely migrate along sequences that are
inverted repeats (the antiparallel stacked-X junction proposed from solution stud ies is
structurally locked and cannot migrate). It is notsurprising, therefore, that the structures of the
junctions in complex with proteins that require scanning along a sequence are in this open-X
conformation.

By combining solution studies with molecular modeling, a model of the stacked-X

junction as derived in which the coaxially stacked arms are related by a positive rotation through
the junction crossover (positive being defined by holding one stacked duplex in front fixed, and
rotating the back duplex in a right-handed direction). This interduplex angle (IDA) has been
estimated directly by low-resolution methods such as gel mobility, atomic force microscopy
(AFM) and fluorescence resonance energy transfer (FRET) spectroscopy.

DNA-Nanomechanical device designed by Seeman

The goals of nanotechnology include nanorobotics. Machines and devices operating at

the nanometer scale have wide variety of exquisite applications ranging from medicine to space
flight, while dramatically reducing the energy and material requirements. The technology that
captures the level of control afforded by biological systems, a level of control which is the basis
of the catalytic, informational, and signal transduction capabilities of proteins and nucleic acids
offers the most promising avenue for building nanoscale machines.

The structural properties that enable DNA to serve so effectively as genetic material can
also be utilized for other purposes. The complementarities that lead to the pairing of the strands
of the DNA double helix can be exploited to assemble more complex motifs, based on branched
structures. Seeman and co-workers at New York University have demonstrated that the level of
control offered by DNA systems can be exploited to make intricate DNA based nanostructures
(Figure 18). These structures have been used as the basis of larger constructions in 2D and 3D.
They made two different nanomechanical devices. These devices range from DNA based shape-

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shifting structures to gears and walkers, a DNA stress-gauge, and even a translation device. The
devices are activated by mechanisms as diverse as small molecules, proteins, and, most
intriguingly, other molecules of DNA.
In the upper portion of the drawing shown below (Figure 19), the connecting bridge is in
the B conformation, so the two helices of the double crossover segments are on the same side of
the helix containing the bridge. In the lower portion, the bridge is in the Z conformation, so the
helices are on opposide sides of the helix. The change from B-DNA to Z-DNA is caused by the
addition of Hexaamminecobalt (III) chloride to the solution. The change back is caused by
removal of this reagent. The two large stippled circles represent fluorescent dyes attached to the
device. The change of conformation from B-DNA to Z-DNA is monitored by fluorescence
resonance energy transfer (FRET) spectroscopy involving these two dyes.

Figure 18 DNA-Nanomechanical device designed by Seeman

B-Z transition of DNA antiparallel double crossover has led to make use of it as a DNA
nanomechanical device. The device works by utilizing the B-Z transition of DNA, it connected
two double crossover molecules by a bridge segment that contains a region that can be converted
from right-handed B-DNA to left-handed Z-DNA.

Force Measurements in Simple Protein and Polymerase

Force measurements provide powerful means of directly quantifying the complex

interactions that determine the properties of biological molecules and biomaterials. The
formation of relatively strong attractive forces between poly ethylene glycol (PEG) and protein is
a good example. At low compressive loads, the forces were repulsive, but they became attractive

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when the proteins were pressed into the polymer layer at higher loads. The adhesion was
sufficiently robust that separation of the streptavidin and PEG uprooted anchored polymer from
the supporting membrane. These interactions altered the properties of the grafted chains. After
the onset of the attraction, the polymer continued to bind protein for several hours. The changes
were not due to protein denaturation. These observation demonstrate directly that the biological
activity of PEG is not due solely to properties of simple polymers such as the excluded volume.
It is also coupled to the competitive interactions between solvent and other materials such as
proteins for the chain segments and to the ability of this material to adopt higher order intrachain
structures.
DNA Complexes

DNA when complexed with protein is called chromatin and chromatin in its condensed
form is called chromosomes. Chromosomes are located in nucleus. Thus within chromosomes,
DNA is held in complexes with structural proteins (Figure 19).

Figure 19 Chromatin and Condensed Chromosome Structure

In eukaryotes, each DNA strand wraps around groups of small protein molecules
called histones, forming a series of bead-like structures, called nucleosomes, connected by the
DNA strand (as illustrated in Figure 19). Under the microscope, uncondensed chromatin has a
"beads on a string" appearance. The string of nucleosomes, already compacted by a factor of six,
is then coiled into an even denser structure known as a solenoid that compacts the DNA by a
factor of 40. The solenoid structure then coils to form a hollow tube. This complex compression

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and structuring of DNA serves several functions. The overall negative charge of the DNA is
neutralized by the positive charge of the histone molecules, the DNA takes up much less space,
and inactive DNA can be folded into inaccessible locations until it is needed.

DNA binding proteins have a central role in all aspects of genetic activity. It is therefore
extremely important to examine the nature of complexes that are formed between proteins and
DNA. The classification of protein-DNA complex is based on the structure of the DNA-binding
regions in the proteins. The helix-turn-helix (HTH), the ββα zinc finger, and the zipper type
motifs are the common types.

Molecular Recognition

“Molecular recognition” which became a popular phrase in the early 1980s, covers a set
of phenomena that may be more precisely but less economically described as being controlled by
specific non-covalent interactions. Such phenomena are crucial in biological systems, and much
modern chemical research is motivated by the prospect that molecular recognition by design
could lead to new technologies.
The term molecular recognition refers to the specific interaction between two or more
molecules through non-covalent bonding such as hydrogen bonding, metal coordination,
hydrophobic forces, Van der Waals forces, π-π interactions, halogen bonding, electrostatic and/or
electromagnetic effects. In addition to these direct interactions as well solvent can play a
dominant indirect role in driving molecular recognition in solution. The host and guest involved
in molecular recognition exhibit molecular. In other words, molecular recognition is one of the
key concepts of supramolecular chemistry. It is distinguished from nonspecific molecular
interaction by its selective nature. Molecular recognition is based on the presence in a molecule
(receptor, or “host”) of a selective binding site to another molecule (ligand, or “guest”) and on
molecular complementary between receptor and ligand, i.e. structure and energy matching.
Molecular recognition plays an important role in biology and mediates interactions
between receptors and ligands, antigens and antibodies, nucleic acids and proteins enzymes and
substrates and nucleic acids with each other. A number of artificial systems have also been
synthesized that depend on molecular recognition, for example, peptide nucleic acids and other
antisense oligonucleotides.

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DNA Based Sensor
A biosensor is an analytical device, used for the detection of an analyte, that combines a
biological component with a physicochemical detector. Deoxyribonucleic acids (DNA) are
arguably the most important of all biomolecules. The unique complementary structure of DNA
between the base pairs has been the basis for genetic analysis. The ability of a single stranded
DNA (ssDNA) molecule to ‘seek out’, or hybridize to, its complementary strand in a sample is
the foundation of DNA-based detection systems.
DNA-based sensors belong to chemical sensors used in chemical/biochemical analysis.
There are some specific features at these sensors regarding their use to the investigation of DNA
itself, both its amount (concentration) and chemical / biochemical reactivity. With respect to this,
the DNA biosensors represent irreplaceable testing devices. From the discovery of
electrochemical activity of nucleic acids by Palecek at the end of the 1950‘s, huge progress can
be observed, particularly at the development of electrochemical DNA biosensors based on the
concept of chemically modified electrodes. Together with an economic prospect, these devices
have already achieved extremely high analytical sensitivity detecting, for instance, femtograms
of original genomic target DNA.

The development of single-use sensors based, for instance, on screen printing technology
is of practical interest for routine analysis. The different type of DNA biosensors are given below
(Table 1).

Table 1 The different types of biosensors

Type of sensor Biological element Transducer

Optical DNA
Fiber optics Optical fiber
Surface Plasmon resonance Resonant mirror
Biomolecular interaction analysis BAIcore
Ramen Spectroscopy SERG probes
Electrochemical DNA Carbon paste electrodes
Piezoelectric DNA
Frequency Crystals
Acoustics Crystals

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 Screening of host-guest interactions of the surface attached DNA has found an interest
among pharmaceutical and medical chemists as well as in environmental research. High
sensitivity typical for the detection of DNA structural changes and damage is of great and unique
importance in various fields. Regarding DNA hybridization, miniaturized DNA chips were
created. The DNA microarrays integrated in multiple biosensors should lead to the simultaneous
analysis of samples with different analytes. Application of nanostructures has been shown as a
way for significant enhancement of the sensitivity of the sensors.
Protein Nano Array
Protein nano array is used for studying interactions between proteins and other molecules
on an extremely small scale. Size is what sets these arrays apart they are built on a nano-scale
(one nanometer equals one-billionth of a meter). The arrays are coated surfaces containing
proteins that can be exposed to other proteins and structures in order to study their interactions.

Figure 20 Comparison of state-of-art microget spot (∼30 μm dia., left) with a 10 × 10 nano
array of protein domains generated in feasibility study (right). The nano array spot domains
shown here are less than 1 μm in diameter.
An essential element of this new technological platform is termed a nano array, an array
of biological molecules deposited in micron or sub-micron spatial addresses. The nano array is
used to construct nano arrays (Figure-20). In the figure, a 10 × 10 spot nano array of the yeast
replication protein RPC19 is compared to the size of a single state of the art micro array spot.
One hundred molecular binding tests can be placed in the area occupied by a single conventional
micro array spot.
The method used to create the nano arrays of protein with 100 to 350 nm features is
called Dip-pen nanolithography (DPN), it was presented to the World by Piner et al. in 1999.

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This technique involves using an instrument to modify the surface of the arrays, which is a type
of gold film. The Dip-pen nanolithography allows researchers to create high-resolution patterns
on the surface, thereby giving the arrays their sensitivity or nano arrays exhibit almost no
detectable non specific binding of proteins to their passivated portions even in complex mixtures
of proteins and therefore provide the opportunity to study a variety of surface mediated
biological recognition processes.
In this method, the cantilever tip of an atomic force microscope (AFM) coated with some
kind molecules is used to directly write patterns onto the surface. In this way, the AFM tip can
imitate a quill pen dipped in ink, where the coating molecules work as the ink (Figure 21).
Because of this, the method got the name Dip-Pen Nanolithography.

Figure 21 Schematic drawing of the dip-pen nano-lithography process.

The first studies mainly used hydrocarbons with thiol terminal groups (alkanthiols,
mainly 1-octadeconthiol, ODT, and 16-mercaptohexadecanoic acid, MHA) on gold substrates,
because of the good adhesion of the thiol groups to the gold surfaces. To achieve homogeneous
coating of the tip, two methods were used: chemical vapour deposition (CVD) or dipping of the
tip in ODT or MHA solutions followed by N2 or difluorethane blow drying.

The DPN approach for creating protein nano arrays is usually through indirect adsorption
of the protein on a MHA patterned surface. First, a tip is coated with MHA, and the wanted
pattern (usually dots) is written to the surface. Next, before proteins are introduced, the surface
not covered by the MHA pattern need to be passivated to avoid non specific binding of proteins
to the surface. Passivation can for example be done by putting a droplet of a solution of poly
(ethylene glycol), PEG, on the surface which will lead to PEG adsorption between the features in

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the MHA pattern. After rinsing, the desired protein is introduced which leads to specific
adsorption to the MHA molecules (Figure 22).

Figure 22 Schematic diagram of pattern writing, passivation, protein adsorption and antigen
binding.

The adsorbed proteins were ImmunoglobulinG (IgG). After IgG adsorption on the
surface, a solution of anti IgG (antigene G) was introduced to the surface, leading to specific
binding of anti IgG to IgG (Figure 20). By imaging the patterned area before and after anti IgG
binding, an increased height profile of the patterned area can verify the specific anti IgG binding
to IgG.

Nanopipettes

Nanopipette is defined as a pipette that has tip diameters ranging from tens to hundreds of
nanometers. The basic shape of a nanopipette is shown below in Figure 23 (A) and (B) with a
diagram of what the pipette’s tip, shoulder, and stem are in (A).

Figure 23 (A) Illustration of a nanopipette denoting the stem, shoulder, shank, and tip. (B)
Optical micrograph of a nanopipette filled with dye for visualization. (C) Scanning electron
micrograph of a nanopipette in end-on view. The nanopore opening at the tip is visible.

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 This diagram will be useful during later descriptions of pipette dimensions to help
visualize what is being described as well as (C) to differentiate between the inner and outer
diameter of the nanopipette tip. Transition electron microscopy (TEM), among other nano-scale
observation methods, was able to do detailed investigations of the structure of these nanopipettes
and indicated that the potential precision, accuracy, and sensitivity had increased greatly over
micropipettes. As the nanopipette tip shrank into the nanometer range, it became viable to apply
an electric potential across the tip to trap negatively charged particles. If this potential was
reversed in polarity, then the particles held within the nanopipette would have been forced out
and delivered to their destination.

Glass Based Nanopipettes

Nanopipettes made of glass are one of the main types of pipette. These pipettes are
similar in nature to the glass micropipettes that chemists and biologists have been using for
decades and are formed by heating a glass capillary in a specific region with either gas heat or
laser radiation. While the glass is being heated, a pulling force is applied to the capillary, usually
by a spring, and a nanopipette is formed in the process as shown in (figure 24) below. One of the
most used methods is the laser heating because it can be used to heat a very specific region of the
capillary and can be turned on and off very quickly. These glass nanopipettes can either be of
quartz or borosilicate base material, and are commonly used as a delivery system for medication
or as a probe to study properties of cells and organelles.

Figure 24 Laser heating and pulling process of a glass capillary to form a micro/nano pipette.

While glass nanopipettes are relatively easy to manufacture and work well as probes for
SPM, they lack features that carbon nanopipettes are known for, such as mechanical robustness,
conductivity, and smaller dimensions which may be useful for interactions with living cells.

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Glass nanopipettes tend to range from 10-200 nm for the inner diameter to 200-500 nm for the
outer diameter.
Glass nanopipette can be coated with conductive material to give the pipette conductive
properties and then baked to attach this coating to the surface. This allows for electrical
experiments and data to be recorded and used to identify cell and tissue properties. Another
potential application is to use these nanopipettes for nanolithography to deliver tiny amounts of a
specific chemical to create the patterns necessary for the procedure.

Carbon Nanopipettes

Carbon nanopipettes (CNPs) are the other main type of nanopipettes that are being
heavily researched and manufactured. The earlier CNPs were realized when carbon-based
nanostructures of tapered whiskers were found to be hollow and have a uniform passageway
through which fluids could potentially be passed through (Figure 25). The ability to reproduce
carbon nanotubes became easier, the current form of carbon nanopipettes was designed. These
recent CNPs are quite different from there glass counterpart’s even if most of the CNPs being
fabricated today included glass pipettes in their design as a template. An alternative form of
fabrication for CNPs is to generate carbon nanotubes and seal them into glass micropipettes for
use. This type of fabrication requires the ability to manipulate single carbon nanotubes and then
assemble the nanopipette, which reduced its ability to be manufactured on a large scale.

Figure 25 SEM images of the pipettes before (A) and after (B) carbon deposition. Scale bars are
100 nm.
Carbon nanopipettes on the other hand involve a longer fabrication process because
instead of just using a laser heating and pulling method, the carbon tube must be deposited on the

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inside of a template and then exposed. While the fabrication process may be less streamlined, the
potential applications for intracellular injections expand greatly over glass nanopipettes. CNPs
also can be used for both injection and probing requirements at the same time and have the
ability to use their mechanical properties to their benefit.

Molecular Diodes

Due to the huge power consumption and expensive fabrication methods required, down
scaling silicon devices to sub-100 nm dimensions is becoming very unattractive. On the other
hand, it is easier to build electronic circuits using molecules since they are small and their
functionality hence properties can be tuned can be tuned. Silicon devices operate based on the
movement of a large number of electrons n bulk matter while molecular devices take advantage
of the quantum mechanical effects taking place at the nanometer scale. The building blocks of
molecular electronics are single or small packets of molecules.
The most important molecular backbones are: 1) polyphenylene-based chains and 2)
carbon nanotubes (Figure 26). Polyphenylene based molecular conductors are made up of
organic aromatic benzene rings with bonds or tied up by acetylene spacers. SWCNT acts as an
ideal quantum wire with current conduction taking place only in one dimension. Unlike in the
case of conventional metallic conductors such as copper, in CNT carriers can only be
backscattered giving rise long range mean free path length. Therefore, in a CNT conduction is
possible only in forward or backward direction since there is significantly reduced phase space
for small angle scattering events in a 1-D system. Monolayer carbon nanotubes have been shown
to outperform copper interconnects.

Polyphenylene chain

Polyphenylene chain in whcih phenyl and phenyene Single wall carbon nanotube.
groups separated

Figure 26 Conducting unit of a molecular diode

In an aliphatic organic molecule with only sigma bonds, the conducting channel outside
the plane of the nuclei has interruptions resulting in discontinuities in the electron density at the
positions of the nuclei. As a result, in the presence of an applied voltage, these molecules cannot
conduct current and act as insulators. Therefore, in the polyphenylene chain, the conductive
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channel can be broken up by inserting an aliphatic molecule leading to the formation of
insulators or barriers to the electron transport.
There are two types of molecular diodes – rectifying diodes and resonant tunneling
diodes. In both these devices, when the applied voltage exceeds a critical value, electrons are
driven through one or more potential barriers.
Molecular Rectifying Diode
A diode or a rectifier, which conducts only in one direction, is the building block of any
three terminal semiconductor electronic device such as a bipolar transistor or a field effect
transistor. The structure of the mono-molecular diode proposed in is shown in first part of Fig. 27
and its schematic representation is shown in second part of Figure 27.

Figure 27 Structure of molecular diode integrally embedded in a poly-phenylene based

molecular conducting wire
This diode is based on a molecular conducting wire consisting of two identical sections
(S1, S2) separated by an insulating group R. Section S1 is doped by at least one electron
donating group (X e.g. –NH2, –OH, –CH3, –CH2CH3) and section S2 is doped by at least one
electron withdrawing group (Y e.g. –NO2, –CN, –CHO). The insulating group R (such as –CH2–,
–CH2CH2–) can be incorporated into the molecular wire by bonding a saturated aliphatic group
(no pi-orbitals). To adjust the voltage drop across R, multiple donor/acceptor sites can be
incorporated. The single molecule ends are connected to the contact electrodes e.g. gold. There
are three potential barriers - one corresponding to the insulating group (middle barrier) and two
corresponding to the contact between the molecule and the electrode (left and right barriers).
These potential barriers provide the required isolation between various parts of the structure. The
occupied energy levels in the metal contacts and the Fermi energy level EF are also shown. On
the left of the central barrier all the pi-type energy levels (HOMO as well as LUMO) are elevated

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due to the presence of the electron donating group X and similarly on the right of the central
barrier the energy levels are lowered due to the presence of the electron withdrawing group Y.
This causes a built-in potential to develop across the barrier represented by the energy difference
DELUMO. For current to flow electrons must overcome the potential barrier from electron
acceptor doped section (S2) to electron donor doped section (S1) and this forms the basis for the
formation of the mono-molecular rectifying diode.
Molecular Resonant Tunneling Diode
Resonant tunneling diodes or RTDs are well known and have been studied widely
because of their potential in very high speed/functionality circuits and as a promising
nanoelectronic device used in analog and digital applications. RTDs have been fabricated using
the semiconductor hetero structure epitaxial techniques to realize the peak current-voltage
characteristics that are typical of tunnel diodes but without the associated problems of large
junction capacitance.

Figure 28 Structure of molecular resonant tunnelling diode

Figure 29 Band diagram of the molecular RTD showing ‘OFF’ and ‘ON’ state.
The structure of a molecular resonance tunneling diode based on a molecular conducting
wire backbone is shown in Figure 28. In this structure, two aliphatic methylene groups (CH2) are
inserted on both sides of the benezene ring. Since aliphatic groups act as insulators, they create
potential barriers to the flow of electrons in the molecular conducting wire. The only way for the

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current to flow in the presence of an applied voltage is when the electrons are forced to pass
through the benezene whose width is only about 0.5 nm. The operation of the molecular RTD
can be understood using the band diagram shown in Figure 29 which shows (i) potential barriers
due to the two aliphatic methylene groups, (ii) energy levels in the benzene ring through electron
must traverse and (iii) the orbital energy levels in the molecular conducting wire.
In the presence of an applied voltage across the molecule, the molecular RTD will not
conduct any current or will remain in OFF state since, as shown in Fig. 30, the kinetic energy of
the incoming electrons is different from that of the empty energy levels inside the benzene ring
sandwiched between the two thin potential barriers. However, by changing the applied voltage a
resonance situation can be created i.e. the kinetic energy of the incoming electrons can be made
to match with one of the unoccupied energy levels inside the benzene ring. The device will now
turn ON since electrons can traverse through the wire Fig. 30. The molecular RTD shows a
negative differential resistance with two operating points following the standard mechanism of a
solid state resonant tunneling diode.
The above discussed molecular diode and molecular RTD can be used as the basic
building blocks for synthesizing a single molecule exhibiting simple Boolean logic such as OR,
AND and XOR gates. By building larger single molecule structures using the above building
blocks, we can even realize more complex digital circuits such as HALF and FULL adders and
their derivatives.
The main advantage of molecular electronics is the lower cost, compatibility with flexible
substrates and simpler packaging when compared to the conventional inorganic electronics.
Unlike in the case of silicon technology, the bottom-up approach of manipulating molecules is
expected to be not only cheap but also will result in higher speeds of information processing with
less power.
Self Assembled Nano Transistors
The push to shrink electronic circuits to ever smaller dimensions is relentless. A
nanotransistor is a transistor - the component that acts as an electronic signal switch or amplifier
- that is near the scale of a billionth of a meter (or nanometer) in size (Figure 30). About 10
million of such nanotransistors would fit on the head of a pin. The characteristic properties of
carbon nanotubes make them the ideal candidate material for many applications in
microelectronics: the tubes carrying electrical current virtually without friction on their surface

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and can therefore handle 1000 times more than copper wire. Interestingly they can be both
conducting and semiconducting. Carbon nanotube transistor can deliver currents in excess of 15
µA at a supply voltage of only 0.4 V (0.7 V is currently the norm), a current density some 10
times above that of silicon.

Figure 30 Structure of a typical nano transistor and CNT nano transistor

Self-assembly is a process in which organization of colloidal, macromolecular, or
supramolecular units into the desired system occurs through nature-intended phenomena, either
mediated by physicochemical pathways or assisted by biomolecules to promote molecular
selectivity and specificity. A functional electronic nano-device has been manufactured using
biological self-assembly. The construction capabilities of DNA and the electronic properties of
carbon nanotubes were harnessed to create the self-assembling nano-transistor.
It involves two step process. First step consists of coating a central part of a long DNA
molecule with proteins from an E. coli bacterium. Next, graphite nanotubes coated with
antibodies were added, which bound onto the protein. After this, a solution of silver ions was
added. The ions chemically attach to the phosphate backbone of the DNA, but only where no
protein has attached. Aldehyde then reduces the ions to silver metal, forming the foundation of a
conducting wire. To complete the device, gold was added. This nucleates on the silver and
creates a fully conducting wire. The end result is a carbon nanotube device connected a both
ends by a gold and silver wire. Thus the DNA molecule was turned into a conducting wire. The
device operates as a transistor when a voltage applied across the substrate is varied. This causes
the nanotubes to either bridge the gap between the wires – completing the circuit – or not. Thus
construction capabilities of DNA and the electronic properties of carbon nanotubes were
combined to create a self-assembling nano-transistor. Self-assembled nanotube field-effect
transistors could be used as label-free protein biosensors as in the case of biotin-streptavidin pair,
nano-scale electronic devices such as computer chips and photonic devices.

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Nanoparticle Mediated Transfections
Transfection is the process of deliberately introducing naked or purified nucleic acids by
non-viral methods into eukaryotic cells. It may also refer to other methods and cell types,
although other terms are preferred: "transformation" is more often used to describe non-viral
DNA transfer in bacteria and non-animal eukaryotic cells, including plant cells. In animal cells,
transfection is the preferred term as transformation is also used to refer to progression to a
cancerous state (carcinogenesis) in these cells. Transduction is often used to describe virus-
mediated gene transfer into eukaryotic cells. A direct approach to transfection is the gene gun,
where the DNA is coupled to a nanoparticle of an inert solid (commonly gold), which is then
"shot" directly into the target cell's nucleus.
Nanoparticle-based transfection reagents are an emerging trend to ensure high efficiency
transfection systems. Transfection, the process of introducing foreign nucleic acids into host
cells, is one of the most powerful Molecular Biology tools currently in use. As the exogenous
DNA/ RNA become functional in transfected cells, they exhibit specific behavior otherwise not
demonstrated by normal cells. The technology is extensively used in studying cellular events and
gene expression, designing knockout systems, developing drugs and conceiving therapeutic
strategies.
Several non-viral transfection methods for eukaryotic cells are used to introduce
membrane impermeable molecules into the cells. However, the efficiency, toxicity, and
reproducibility, which may vary depending on the characteristics of the cells used, remain a
crucial aspect in cell transfection. Consequently, various methods and modifications are
currently being evaluated to increase efficiency and reduce toxicity. Thus, both novel laser-based
transfection methods as well as nanoparticle (NP).
For example, Petersen et al., (2009) positively charged AuNPs with a DNA plasmid that
encodes recombinant eGFP-C1-HMGB1 fusion protein for 24 hours before cellular transfection
does not seem to alter the protein expression and the protein functionality (DNA binding), while
the presence of AuNPs seems to have a significantly positive effect on the transfection
efficiencies. The observed effect was size-dependent: medium sized AuNPs enhanced
transfection efficiency nearly 6 fold. These results support the hypothesis that laser-generated
AuNPs present a good alternative to chemically synthesized nanoparticles and are especially
suitable for biomedical applications.

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