06 - Chapter 1 PDF

Chapter 1
Introduction: Important Biomolecules
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Ashvin B. Padhiyar / Ph. D. Thesis (Physics) / Sardar Patel University - 2010
Introduction of Biomolecules
It hardly needs to be emphasized that cell is the fundamental unit of
organization through which life is expressed. This cell or unit of life is a
storehouse of multiple information molecules responsible for bioactions.
Interestingly, it is not known with any degree of certainly as to how cells
were first formed, but there is a good deal of evidence to suggest that variety
of chemical and physical processes taking place on the earth or its
surrounding atmosphere, led to the information of simple molecules
representing the cellular status. These biomolecules entered in to a network
of interaction resulting in more and more complex groupings and structures.
Finally these biomolecules formed a concrete organizational unit which
expressed it self in the form of life.
A large number of biomolecules are in living cells. These include
monosaccharides, disaccharides, polysaccharides, amino acids, proteins,
enzymes, fatty acids, fats and oils, nucleotides, nucleic acids, histones, acidic
proteins, chlorophyll, hemoglobin and a multiple of several other
components of cells It is impossible to pinpoint as to which of the myriads of
biomolecule is living, because none of these ,independently, can be
expressive of life. Viruses are perhaps the simplest of living creatures. These
represent the organization of two important biomolecules including protein
and RNA or DNA.
Meaning of Biomolecules
Biomolecules are complex organic molecules. These molecules form
the basic structural constituent of a living cell. The organic compounds such
as amino acids, nucleotides and monosaccharides serve as building blocks of
complex biomolecules. The important biomolecules are proteins,
carbohydrates and fats, enzymes, vitamins, hormones and nucleic acids.
Some of the biomolecules are polymers. For e.g., starch, proteins, nucleic
acids are condensation polymers of simple sugars, amino acids and
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nucleotides respectively. Most of the biomolecules are very large and
extremely complex. Their reactions involve complex mechanisms.
Biomolecules are related to the living organisms in the following sequence;
Types of Biomolecules
There are several types of biomolecules. Of most importance are the
nucleotides that make up DNA and RNA, the molecules that are involved in
heredity. There are also the lipids which function as the building blocks of
biological membranes and as energy providing molecules. The hormones
serve in the regulation of metabolic processes and many other roles in
organisms. The carbohydrates are also important in the provision of energy
and as energy storage molecules. Amino acids and proteins function in many
capacities in living organisms which include the synthesis of proteins, in the
genetic code and as biomolecules that assist in other processes such as lipid
transport. Vitamins are also necessary to the survival and health of
organisms and though not synthesized by organisms but are important
biomolecules.
- A diverse range of biomolecules exist, including:
Small molecules:
Lipids, phospholipids, glycolipids, sterols, glycerolipids
Carbohydrates, sugars
Vitamins
Hormones, neurotransmitters
Metabolites
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Monomers:
Amino acids
Nucleotides
Monosaccharides
Polymers:
Peptides, oligopeptides, polypeptides, proteins
Nucleic acids, DNA, RNA
Oligosaccharides, polysaccharides (including cellulose)
Cellulose, lignin
Hemoglobin
Areas of Biomolecules
The study of biomolecules is closely related to several fields such as
molecular biology, biochemistry and genetics. Biochemistry is the study of
the structure and function of biomolecules in organisms. This study has
revealed a wealth of information about the biomolecules in living things.
Processes such as glycolysis have been detailed by biochemical studies
which have identified the roles of the biomolecules and their importance. It
was previously thought that the molecules of life, biomolecules, could only
be produced by living organisms. This view was however dispelled with the
synthesis of urea. Today, a focus of biochemistry is the study of enzymes,
biomolecules that are made up of proteins. These biomolecules are essential
to organisms as they speed up reactions that would normally take too long to
sustain life.
Biomolecules obeys the conservation laws of physics for exchange of
energy:
In nature, there is continuous process of exchanging the energy by some kind
of process into the matters; this becomes possible because of some matter
which loses their energy while the others gain the energy.
Straight forword the biomolecules also take part in that process of
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exchanging their energy. This process is very important to growth as well as
to maintain their characteristics to do the living processes. Now the question
is arising into mind that how these processes are possible. To understand it,
we take example of non living molecules and the process of exchange of
energy. Into the non living molecules the exchange of energy is produced by
the chemical process at specific atmospheric condition. Similarly such kind
of process occurs for the biomolecules or living molecules. In such process,
the energy is absorbed by molecules in some form from the environment and
it is utilized for growth of itself. This becomes possible. In the specific
condition of atmosphere means at particular temperature and specific
pressure. That energy which is not utilized by it is released into the
environment.
This utilized energy can do work by molecules at a given specific
condition. Here such kind of biomolecules work differently rather than the
non-bio molecules, e.g. into the non-biological molecules can do this process
under the extreme conditions like high temperature, high pressure, into the
strong electric and magnetic field region as well as into the biomolecules
which are restricted to do that process into such kind of condition.
Biomolecules are consisting of the cells and these cells play
important role to do the different kind of the process including the exchange
of energy by any kind of process. Biomolecules are consisting of cells which
are carrying large numbers of chemicals. This chemical consisting energy is
used to do different kind of activities like growth and repair of biomolecules.
The nonliving or nonbiomolecules got their energy by different
processes, which have different sources of the energy while for the
biomolecules are directly or indirectly got their energy from the sunlight and
that is important source of energy for biomolecules. e. g. The cells of the
plants are grown by gaining their energy from the sunlight. This becomes
possible by the photosynthesis process when it is produced by the cells of the
plant. Into this process, the conversion of carbon dioxide into the water
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provides the different form of energy to the cells of the plant which is
utilized for the different purposes.
The biomolecules are present into the bacteria, plant, animals in
which exchange of energy occur through the environment, so we can say that
the physical rules are also followed by the biomolecules for their growth,
stability, maintenance, repair and for the many type of the other purposes.
1.1.1 Starch and Cyclodextrins (Carbohydrates)
Starch
Starch or amylum is a polysaccharide carbohydrate consisting of a
large number of glucose units joined together by glycosidic bonds. Starch is
produced by all green plants as an energy store. It is the most important
carbohydrate in the human diet and is contained in such staple foods as rice,
wheat, maize (corn), potatoes and cassava.
Pure starch is a white, tasteless and odorless powder that is insoluble in cold
water or alcohol. It consists of two types of molecules: the linear and helical
amylose and the branched amylopectin. Depending on the plant, starch
generally contains 20 to 25% amylose and 75 to 80% amylopectin [1].
Glycogen, the glucose store of animals, is a more branched version of
amylopectin.
Starch can be used as a thickening, stiffening or gluing agent when
dissolved in warm water, giving wheat paste.
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Plants store glucose as the polysaccharide starch. The cereal grains
(wheat, rice, corn, oats, and barley) as well as tubers such as potatoes are
rich in starch.
Starch can be separated into two fractions--amylose and
amylopectin. Natural starches are mixtures of amylose (10-20%) and
amylopectin (80-90%).
Amylose forms a colloidal dispersion in hot water whereas

amylopectin is completely insoluble. The structure of amylose consists of
long polymer chains of glucose units connected by an alpha acetal linkage.
Starch - Amylose: Shows a very small portion of an amylose chain. All of
the monomer units are alpha -D-glucose, and all the alpha acetal links
connect C # 1 of one glucose to C # 4 of the next glucose.
Starch has a few other uses other than food. It's used in pressing
clothes to keep them from wrinkling. It's also used to make a foam packing.
Starch is biodegradable, so starch foam packing is an environmentally-
friendly alternative to Styrofoam packing.
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Starch Coil or Spiral Structure
As a result of the bond angles in the alpha acetal linkage, amylose
Starch Coil
actually forms a spiral much like a coiled spring. See the graphic on the left
which show four views in turning from a side to an end view.
Carbohydrates
Carbohydrates, which include the sugars and polysaccharides, have
many important functions in biological systems.
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Carbohydrates are so named because the structural formula is typically
(CH2O)n, where n is an integer such as 5 (C5H10O5),6 (C6H12O6), etc.
Although this formula might suggest that carbon atoms are joined to
water, the actual molecules are more complicated.
Like most classes of biological molecules, carbohydrates occur as both
monomers and polymers. Small carbohydrates are called sugars, which
commonly include monosaccharides (single sugars) and some disaccharides
(two sugars linked together). Larger carbohydrate is called polysaccharide.
(many sugars linked together).
Functions of carbohydrates include:
• serving as precursors for building many polymers
• storing short-term energy
• providing structural building materials
• serving as molecular "tags" to allow recognition of specific cells and
molecules
Monosaccharides are the simplest form of carbohydrates. They
consist of one sugar and are usually colorless, water-soluble, crystalline
solids. Some monosaccharides have a sweet taste. Examples of
monosaccharides include glucose (dextrose), fructose, galactose, and ribose.
Monosaccharides are the building blocks of disaccharides like sucrose
(common sugar) and polysaccharides (such as cellulose and starch). Further,
each carbon atom that supports a hydroxyl group (except for the first and
last) is chiral, giving rise to a number of isomeric forms all with the same
chemical formula. For instance, galactose and glucose are both aldohexoses,
but they have different chemical and physical properties [8].
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1.1.2 Amino acids and Peptides:
Amino acids
All peptides and proteins are polymers of alpha-amino acids. An
amino acid is a molecule that contains both amino (NH2) and carboxyl
(COOH) functional groups. Alanine is one of the standard amino acids:
Amino acids exist in either D (dextro) or L (levo) form

(stereoisomers). The D and L refer to the absolute confirmation of optically
active compounds. With the exception of glycine, all other amino acids are
mirror images that can not be superimposed. Most of the amino acids found
in nature are of the L-type. Hence, eukaryotic proteins are always composed
of L-amino acids although D-amino acids are found in bacterial cell walls
and in some peptide antibiotics.
Amino acids are molecules containing an amine group, a carboxylic
acid group and a side chain that varies between different amino acids. These
molecules are particularly important in biochemistry, where this term refers
to alpha-amino acids with the general formula H2NCHRCOOH, where R is
an organic substituent. In the alpha amino acids, the amino and carboxylate
groups are attached to the same carbon atom, which is called the α–carbon.
The various alpha amino acids differ in which side chain (R group) is
attached to their alpha carbon. These side chains can vary in size from just a
hydrogen atom in glycine, to a methyl group in alanine, through to a large
heterocyclic group in tryptophan [14].
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Twenty Amino Acids
Grouped table of twenty amino acids' structures, nomenclature, and their

side groups' pKa's.
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Naturally occurring amino acids, their abbreviations, and structural formulas
Essential amino acids
Ala = alanine Arg = arginine
CH3CH(NH2)COOH H2N-C(=NH)NHCH2CH2CH2CH(NH2)COOH
Asn = asparagine Asp = aspartic acid

H2N-C(=O)CH2CH(NH2)COOH HOOC-CH2CH(NH2)COOH
Cys = cysteine Gln = glutamine

HS-CH2CH(NH2)COOH H2N-C(=O)CH2CH2CH(NH2)COOH
Glu = glutamic acid Gly = glycine

HOOC-CH2CH2CH(NH2)COOH H2N-CH2COOH
His = histidine *
Ile = isoleucine *
CH3CH2CH(CH3)CH(NH2)COOH
Leu = leucine * Lys = lysine *

CH3CH(CH3)CH2CH(NH2)COOH H2N-CH2CH2CH2CH2CH(NH2)COOH
Phe = phenylalanine *
Met = methionine *
CH3-S-CH2CH2CH(NH2)COOH
Pro = proline
Ser = serine
HOCH2CH(NH2)COOH
Trp = tryptophan *
Thr = threonine *
CH3CH(OH)CH(NH2)COOH
Tyr = tyrosine
Val = valine *
CH3CH(CH3)CH(NH2)COOH
Amino acids are critical to life, and their most important function is
their variety of roles in metabolism. One particularly important function is as
the building blocks of proteins, which are linear chains of amino acids.
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Every protein is chemically defined by this primary structure, its unique
sequence of amino acid residues, which in turn define the three-dimensional
structure of the protein. Just as the letters of the alphabet can be combined to
form an almost endless variety of words, amino acids can be linked together
in varying sequences to form a vast variety of proteins.Amino acids are also
important in many other biological molecules, such as forming parts of
coenzymes, as in S-adenosylmethionine, or as precursors for the biosynthesis
of molecules such as heme. Due to this central role in biochemistry, amino
acids are very important in nutrition. Amino acids are commonly used in
food technology and industry. For example, monosodium glutamate is a
common flavor enhancer that gives foods the taste called umami [4].
The term "essential amino acid" refers to an amino acid that is
required to meet physiological needs and must be supplied in the diet.
Arginine is synthesized by the body, but at a rate that is insufficient to meet
growth needs. Methionine is required in large amounts to produce cysteine if
the latter amino acid is not adequately supplied in the diet. Similarly,
phenylalanine can be converted to tyrosine, but is required in large quantities
when the diet is deficient in tyrosine. Tyrosine is essential for people with
the disease phenylketonuria (PKU) whose metabolism cannot convert
phenylalanine to tyrosine. Isoleucine, leucine, and valine are sometimes
called "branched-chain amino acids" (BCAA) because their carbon chains
are branched.
Standard amino acids
Amino acids are the structural units that make up proteins. They join
together to form short polymer chains called peptides or longer chains called
either polypeptides or proteins. These polymers are linear and unbranched,
with each amino acid within the chain attached to two neighbouring amino
acids. The process of making proteins is called translation and involves the
step-by-step addition of amino acids to a growing protein chain by a
ribozyme that is called a ribosome.The order in which the amino acids are
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added is read through the genetic code from an mRNA template, which is a
RNA copy of one of the organism's genes. Twenty-two amino acids are
encoded by the standard genetic code and are called proteinogenic or
standard amino acids.
The amino acid selenocysteine
Non-standard amino acids

Aside from the twenty-two standard amino acids, there are a vast number of
"non-standard" amino acids. Two of these can be specified by the genetic
code, but are rather rare in proteins. Selenocysteine is incorporated into some
proteins at a UGA codon, which is normally a stop codon.Pyrrolysine is used
by some methanogenic archaea in enzymes that they use to produce
methane. Other non-standard amino acids found in proteins are formed by
post-translational modification, which is modification after translation in
protein synthesis. These modifications are often essential for the function or
regulation of a protein; for example, the carboxylation of glutamate allows
for better binding of calcium cations, and the hydroxylation of proline is
critical for maintaining connective tissues. Another example is the formation
of hypusine in the translation initiation factor EIF5A, through modification
of a lysine residue. Such modifications can also determine the localization of
the protein, e.g., the addition of long hydrophobic groups can cause a protein
to bind to a phospholipid membrane [13].
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1.1.3 Fibrous and Globular Proteins:
In general, we can use the conformation of a protein to classify it into
one of two very broad categories. One of those is fibrous, the other is
globular. The fibrous proteins are generally long and insoluble in water. The
globular proteins are tightly folded and most of them are soluble in water.
Some proteins combine the properties of both fibrous and globular within the
same protein.
Fibrous Proteins
- Stringy, physically tough, generally insoluble in water and most solvents
- Elongated, rod- like proteins joined by several types of cross – linkages.
Globular Proteins
- Generally sphericsl or globuler
- Tend to be soluble in water and aqueous solutions
- Polar groups of the side chains are on the outer side
- Nearly all enzymes, antibodies, hormones and transport proteins are
globular
3-dimensional structure of hemoglobin, a globular protein.

Globular proteins or spheroproteins are one of the three main protein
classes, comprising "globe"-like proteins that are more or less soluble in
aqueous solutions (where they form colloidal solutions). This main
characteristic helps distinguishing them from fibrous proteins (the other
class), which are practically insoluble. [9].
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Globular Structure and Solubility
The term globular protein is quite old and is now somewhat archaic
given the hundreds of thousands of proteins and more elegant and
descriptive structural motif vocabulary. The globular nature of these proteins
can be determined without the means of modern techniques, but only by
using ultracentrifuges or dynamic light scattering techniques.
A wide range of roles in the organism
Unlike fibrous proteins which only play a structural function,
globular proteins can act as:
Enzymes, by catalyzing organic reactions taking place in the organism
in mild conditions and with a great specificity. Different esterases fulfill this
role.
Messengers, by transmitting messages to regulate biological
processes. This function is done by hormones, i.e. insulin etc. [7].
Structure of Proteins
Three possible representations of the three-dimensional structure of the protein triose

phosphate isomerase. Left: all-atom representation colored by atom type. Middle: Simplified
representation illustrating the backbone conformation, colored by secondary structure. Right:
Solvent-accessible surface representation colored by residue type (acidic residues red, basic residues
blue, polar residues green, nonpolar residues white).
Most proteins fold into unique 3-dimensional structures. The shape

into which a protein naturally folds is known as its native conformation.
[17].Although many proteins can fold unassisted, simply through the
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chemical properties of their amino acids, others require the aid of molecular
chaperones to fold into their native states [18]. Biochemists often refer to
four distinct aspects of a protein's structure [19].
Primary Structure: the amino acid sequence.
Secondary Structure: regularly repeating local structures stabilized by
hydrogen bonds.
The most common examples are the alpha helix, beta sheet and turns.
Because secondary structures are local, many regions of different secondary
structure can be present in the same protein molecule.
Tertiary Structure: the overall shape of a single protein molecule; the
spatial relationship of the secondary structures to one another. Tertiary
structure is generally stabilized by nonlocal interactions, most commonly the
formation of a hydrophobic core, but also through salt bridges, hydrogen
bonds, disulfide bonds, and even post-translational modifications. The term
"tertiary structure" is often used as synonymous with the term fold. The
Tertiary structure is what controls the basic function of the protein [15]
Quaternary Structure: the structure formed by several protein molecules
(polypeptide chains), usually called protein subunits in this context, which
function as a single protein complex.
Proteins are not entirely rigid molecules. In addition to these levels of
structure, proteins may shift between several related structures while they
perform their functions. In the context of these functional rearrangements,
these tertiary or quaternary structures are usually referred to as
"conformations", and transitions between them are called conformational
changes. Such changes are often induced by the binding of a substrate
molecule to an enzyme's active site, or the physical region of the protein that
participates in chemical catalysis. In solution proteins also undergo variation
in structure through thermal vibration and the collision with other molecules.
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1.1.4 Vitamins & Enzymes
Vitamins
From the beginning, humans ate primarily whole foods or so-called
"natural" foods, which underwent no processing. The nutrient content of
food is decreased when it is processed. Intensive animal rearing,
manipulation of crop production, and food processing have altered the
qualitative and quantitative balance of nutrients of foods consumed by the
Western world. This change is possibly one of the reasons that chronic,
debilitating diseases are rampant in our modem culture. Modem research
suggests that simply taking a synthetic multi-vitamin/mineral formula does
not change this. Research from around the globe asserts that vitamins in their
naturally-balanced state are essential for better assimilation, synergistic
action, and maximum biological effect. And yet most consumers buy
vitamins and minerals that are synthetic, which their bodies usually can't
assimilate properly. The U.S. National Academy of Science, Food and
Nutrition Board, recommends that people meet their daily nutritional needs
through a varied diet rather than through vitamin and mineral
supplementation [6].
A lot of people think vitamins can replace food. They cannot. In fact,
vitamins cannot be assimilated without ingesting food. That is why we
suggest taking them with a meal. Vitamins help regulate metabolism, help
convert fat and carbohydrates into energy, and assist in forming bone and
tissue.
Forms of Vitamins Supplements and how they work?
Over-the-counter vitamin supplements come in various forms,
combinations, and amounts. They are available in tablet, capsule, gel-
capsule, powder, sublingual, lozenge, and liquid forms. They can also be
administered by injection. In most cases, it is a matter of personal preference
as to how you take them; however, due to slight variations in how rapidly the
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supplements are absorbed and assimilated into the body, we will sometimes
recommend one form over another.
Vitamin supplements are usually available as isolated vitamins or in
combination with other nutrients. It is important to select your vitamins
based upon what you really need. A program designed for health
maintenance would be different from one designed to overcome a specific
disorder. If you find one supplement that meets your needs, remember to
make it daily. If it does not contain a large enough quantity of what you
want, you may consider taking more than one.If there is no single
supplement that provides you with what you are looking for, consider taking
a combination of different supplements. Because the potency of most
vitamins may be decreased by sunlight, make sure that the container holding
your vitamins is dark enough to shield its contents properly. Some people
may be sensitive to plastic, and may need to purchase vitamins in glass
containers. Vitamin supplements should be kept in a cool, dark place. All
vitamin supplements work best when taken in combination with food. Unless
specified otherwise, oil-soluble vitamins should be taken before meals, and
water-soluble ones should be taken after meals.
Vitamins have traditionally played the role of coenzymes, organic
molecules that facilitate the chemical reactions catalyzed by enzymes.
However, several vitamins assume additional endocrine-like actions; this
review will discuss four such vitamins. Vitamin K2 is involved in the
gamma-carboxylation of coagulation factors and bone proteins, but it can
also bind and activate the steroid and xenobiotic receptor in order to mediate
transcription in bone tissue, and has been used to treat osteoporosis. Biotin is
critical for some carboxylation reactions, but it also induces epidermal
differentiation and has been used to treat lameness in animals and brittle
nails in humans. Pyridoxal phosphate (the active form of vitamin B6) is
involved in a multitude of reactions, including decarboxylation and
transamination; it can also inhibit DNA polymerases and several steroid
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receptors and may prove useful as an adjunct in cancer chemotherapy.
Finally, nicotinic acid is converted to NAD+ and NADP+, which are used as
hydrogen/electron carriers in redox reactions. However, it also possesses
vasodilatory and antilipolytic activities [8].
Vitamins are miracle workers in the body, but they do not work
alone.Our bodies were created to be able to convert food into energy but in
order to do this it needs three critical elements. Used together, they are
Vitamins, minerals, and enzymes.
Enzymes are tiny elements found in all cell of any living organism,
plant, animal, human. Enzymes are the catalysts, which speed up our body
processes and functions. Think of an enzyme as a specialist. It has one task
to perform, create energy from vitamins in our foods. Here is the next
important bit of information about your friend the Enzyme; he cannot live in
temperatures over 120 degrees. If you cook the foods over that, the enzymes
in the foods will be killed by the heat, and no longer an added source. Foods
that are good tasting, raw, should be eaten as much as possible in the diet.
There are two kinds of Vitamins: Those which dissolve in fat (such
as in eggs and liver); and those which dissolve in water (like in fruits and
vegetables). The fat soluble vitamins are A, D, E, and K. The water soluble
one are C, various B complex, P and others. Vitamins A and D are the two
vitamins which are stored in the liver for future use, as well as some others
we will discuss later. So beware of these levels, as excessive amounts, could
cause trouble. As a general rule of thumb, 50,000 IU or Vitamin A and
4,000 Units of Vitamin D, are considered safe. Please check with your own
physician before taking any medications [7].
As our body uses the vitamin supply by its own activity, what can
you do to help keep your sources of vitamins at higher levels? Replace them
with high vitamin sources of foods, and read the list below. This is only a
small list of items which deplete our vitamins:
Tobacco, alcohol
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salt, sugar, rancid fats
estrogen antibiotics
sleeping pills, tranquilizers
mineral oil
surgery sickness, accidents
emotional strain
fluorides
polluted air or water
pesticides
Vitamins and Minerals
Vitamin A - antioxidant, good for skin, night vision, fighting infections.
Spinach, green leafy veg, peppers, yellow veg, fruit, dried apricots,
watercress, tomatoes, broccoli, and asparagus.
B group - B1- energy production, B2 - converts fats, sugar, proteins to
energy, B3 - energy production, skin, balancing blood sugar, B5 - energy
production, metabolism of fats, healthy skin and hair, B6 - using proteins.
Green leafy veg, avocadoes, mushrooms, currants, watercress, courgette
(zucchini), asparagus, mushrooms, peppers, tomatoes, broccoli, lentils,
onions, seeds and nuts.
B12 - for using proteins.
Seaweed, unpasteurised miso, spirulina, chlorella, fermented foods,
unwashed produce.
Biotin - helps to use essential fats.
Lettuce, tomatoes, almonds.
Vitamin C - antioxidant, protects immune system.
Green leafy veg, peppers, broccoli, parsley, potatoes, watercress, melon,
tomatoes.
Vitamin D - bones, teeth.
Sunlight.
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Vitamin E - antioxidant, helps skin.
Tahini, nuts and seeds, avocadoes.
Folic Acid - brain/nerves
Spinach, asparagus, sesame seeds, hazelnuts, broccoli, avocadoes.
Vitamin K - blood clotting.
Green leafy veg, seaweeds.
Iron - blood, energy.
Avocadoes, dried figs, deep green veg, spinach, parsley, dates, dried
apricots, chickpeas (garbanzo beans), almonds, brazil nuts, sesame seeds.
Calcium - bones, skin, heart, muscles.
Tahini/sesame seeds, green leafy veg, parsley, broccoli, almonds, brazil nuts,
chia seeds.
Zinc - growth, nerves, bones, hair, energy.
Sesame seeds/tahini, almonds, ginger, brazil nuts.
Iodine - thyroid function.
Green leafy veg, seaweeds.
Magnesium - bones, energy.
Green leafy veg, almonds, broccoli, brazil nuts, garlic.
Phosphorus, Sulphur - growth, maintenance, tissues.
Chickpeas (garbanzo beans), many fruits and veg, peas, onion, garlic.
Potassium - nutrient flow, energy, metabolism.
Many fruits and veg (esp. bananas), watercress, parsley, courgettes,
mushrooms, Selenium - antioxidant, metabolism.
Brazil nuts, mushrooms, courgette (zucchini).
Bioflavonoids - aid Vitamin C uptake, bruise healing.
Berries, limes, lemons, peppers, tomatoes, grapes.
Choline - helps break down fat.
Whole grains, nuts, pulses.
Co-Enzyme Q10 - energy, metabolism.
Spinach, sesame seeds.
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Enzymes
A catalytic protein produced by living cells. The chemical reactions
involved in the digestion of foods, the biosynthesis of macromolecules, the
controlled release and utilization of chemical energy, and other processes
characteristic of life are all catalyzed by enzymes. In the absence of
enzymes, these reactions would not take place at a significant rate. Several
hundred different reactions can proceed simultaneously within a living cell,
and the cell contains a comparable number of individual enzymes, each of
which controls the rate of one or more of these reactions. The potentiality of
a cell for growing, dividing, and performing specialized functions, such as
contraction or transmission of nerve impulses, is determined by the
complement of enzymes it possesses. Some representative enzymes, their
sources, and reaction specificities are shown in the table [11].
Characteristics
Enzymes are such efficient catalysts that they accelerate chemical
reactions measurably, even at concentrations so low that they cannot be
detected by most chemical tests for protein. Like other chemical reactions,
enzyme-catalyzed reactions proceed only when accompanied by a decrease
in free energy; at equilibrium the concentrations of reactants and products
are the same in the presence of an enzyme as in its absence. An enzyme can
catalyze an indefinite amount of chemical change without itself being
diminished or altered by the reaction. However, because most isolated
enzymes are relatively unstable, they often gradually lose activity under the
conditions employed for their study.
Chemical Nature
All enzymes are proteins. Their molecular weights range from about
10,000 to more than 1,000,000. Like other proteins, enzymes consist of
chains of amino acids linked together by peptide bonds. An enzyme
molecule may contain one or more of these polypeptide chains. The
sequence of amino acids within the polypeptide chains is characteristic for
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each enzyme and is believed to determine the unique three-dimensional
conformation in which the chains are folded. This conformation, which is
necessary for the activity of the enzyme, is stabilized by interactions of
amino acids in different parts of the peptide chains with each other and with
the surrounding medium. These interactions are relatively weak and may be
disrupted readily by high temperatures, acid or alkaline conditions, or
changes in the polarity of the medium. Such changes lead to an unfolding of
the peptide chains (denaturation) and a concomitant loss of enzymatic
activity, solubility, and other properties characteristic of the native enzyme.
Enzyme denaturation is sometimes reversible.
Many enzymes contain an additional, nonprotein component, termed
a coenzyme or prosthetic group. This may be an organic molecule, often a
vitamin derivative, or a metal ion. The coenzyme, in most instances,
participates directly in the catalytic reaction. For example, it may serve as an
intermediate carrier of a group being transferred from one substrate to
another. Some enzymes have coenzymes that are tightly bound to the protein
and difficult to remove, while others have coenzymes that dissociate readily.
When the protein moiety (the apoenzyme) and the coenzyme are separated
from each other, neither possesses the catalytic properties of the original
conjugated protein (the holoenzyme). By simply mixing the apoenzyme and
the coenzyme together, the fully active holoenzyme can often be
reconstituted. The same coenzyme may be associated with many enzymes
which catalyze different reactions. It is thus primarily the nature of the
apoenzyme rather than that of the coenzyme which determines the specificity
of the reaction [9].
1.1.5 Lipids and Membranes
The boundaries of cells are formed by biological membranes, the
barriers that define the inside and the outside of a cell (shown in below
figure). These barriers prevent molecules generated inside the cell from
leaking out and unwanted molecules from diffusing in; yet they also
24
contain transport systems that allow specific molecules to be taken up and
unwanted compounds to be removed from the cell. Such transport systems
confer on membranes the important property of selective permeability [15].
Membranes are dynamic structures in which proteins float in a sea of
lipids. The lipid components of the membrane form the permeability barrier,
and protein components act as a transport system of pumps and channels that
endow the membrane with selective permeability.
(Red-Blood-Cell Plasma Membrane)

An electron micrograph of a preparation of plasma membranes from
red blood cells showing the membranes as seen “on edge,” in cross section.
In addition to an external cell membrane (called the plasma
membrane), eukaryotic cells also contain internal membranes that form the
boundaries of organelles such as mitochondria, chloroplasts, peroxisomes,
and lysosomes. Functional specialization in the course of evolution has been
closely linked to the formation of such compartments. Specific systems have
evolved to allow targeting of selected proteins into or through particular
internal membranes and, hence, into specific organelles. External and
internal membranes have essential features in common, and these essential
features are the subject of this chapter.
Biological membranes serve several additional important functions
indispensable for life, such as energy storage and information transduction,
that are dictated by the proteins associated with them. In this chapter, we will
25
examine the general properties of membrane proteins—how they can exist in
the hydrophobic environment of the membrane while connecting two
hydrophilic environments—and delay a discussion of the functions of these
proteins to the next.
1.1.6 RNA and DNA – Nucleic acids
- Ribonucleic acid
Ribonucleic acid, or RNA, is a nucleic acid polymer consisting of
nucleotide monomers, which plays several important roles in the processes
of transcribing genetic information from deoxyribonucleic acid (DNA) into
proteins. RNA acts as a messenger between DNA and the protein synthesis
complexes known as ribosomes, forms vital portions of ribosomes, and
serves as an essential carrier molecule for amino acids to be used in protein
synthesis [16]. The three types of RNA include tRNA (transfer), mRNA
(messenger) and rRNA (ribosomal).
- Deoxyribonucleic Acid
DNA
Chemical structure of DNA. Hydrogen bonds shown as dotted lines.

Deoxyribonucleic acid is a nucleic acid that contains the genetic
instructions used in the development and functioning of all known living
26
organisms. The main role of DNA molecules is the long-term storage of
information and DNA is often compared to a set of blueprints, since it
contains the instructions needed to construct other components of cells, such
as proteins and RNA molecules. The DNA segments that carry this genetic
information are called genes, but other DNA sequences have structural
purposes, or involved in regulating the use of this genetic information [11].
DNA is made of four types of bases named cytosine, thymine,
guanine and adenine, which are linked together to form a chain. The bases
are attached to each other in this chain by a sugar-phosphate backbone. Two
of these chains then coil around each other, forming the DNA double helix.
DNA is a long polymer made from repeating units called nucleotides.
The DNA chain is 22 to 26 Angstroms wide (2.2 to 2.6 nanometres), and one
nucleotide unit is 3.3 Å (0.33 nm) long. Although each individual repeating
unit is very small, DNA polymers can be very large molecules containing
millions of nucleotides. For instance, the largest human chromosome,
chromosome number 1, is approximately 220 million base pairs long [14].
In living organisms, DNA does not usually exist as a single molecule,
but instead as a pair of molecules that are held tightly together. These two
long strands entwine like vines, in the shape of a double helix. The
nucleotide repeats contain both the segment of the backbone of the molecule,
which holds the chain together, and a base, which interacts with the other
DNA strand in the helix. A base linked to a sugar is called a nucleoside and a
base linked to a sugar and one or more phosphate groups is called a
nucleotide. If multiple nucleotides are linked together, as in DNA, this
polymer is called a polynucleotide [19].
The backbone of the DNA strand is made from alternating phosphate
and sugar residues [10]. The sugar in DNA is 2-deoxyribose, which is a
pentose (five-carbon) sugar. The sugars are joined together by phosphate
groups that form phosphodiester bonds between the third and fifth carbon
atoms of adjacent sugar rings. These asymmetric bonds mean a strand of
27
DNA has a direction. In a double helix the direction of the nucleotides in one
strand is opposite to their direction in the other strand: the strands are
antiparallel. The asymmetric ends of DNA strands are called the 5′ (five
prime) and 3′ (three prime) ends, with the 5' end having a terminal phosphate
group and the 3' end a terminal hydroxyl group. One major difference
between DNA and RNA is the sugar, with the 2-deoxyribose in DNA being
replaced by the alternative pentose sugar ribose in RNA.
A section of DNA.The bases lie horizontally between the two spiraling strands.
The DNA double helix is stabilized by hydrogen bonds between the
bases attached to the two strands. The four bases found in DNA are adenine
(abbreviated A), cytosine (C), guanine (G) and thymine (T). These four
bases are attached to the sugar/phosphate to form the complete nucleotide, as
shown for adenosine monophosphate [10].
These bases are classified into two types; adenine and guanine are
fused five- and six-membered heterocyclic compounds called purines, while
cytosine and thymine are six-membered rings called pyrimidines. A fifth
pyrimidine base, called uracil (U), usually takes the place of thymine in
RNA and differs from thymine by lacking a methyl group on its ring. Uracil
is not usually found in DNA, occurring only as a breakdown product of
28
cytosine. In addition to RNA and DNA, a large number of artificial nucleic
acid analogues have also been created to study the proprieties of nucleic
acids, or for use in biotechnology [21].
Base pairing
Each type of base on one strand forms a bond with just one type of
base on the other strand. This is called complementary base pairing. Here,
purines form hydrogen bonds to pyrimidines, with A bonding only to T, and
C bonding only to G. This arrangement of two nucleotides binding together
across the double helix is called a base pair. As hydrogen bonds are not
covalent, they can be broken and rejoined relatively easily. The two strands
of DNA in a double helix can therefore be pulled apart like a zipper, either
by a mechanical force or high temperature [22]. As a result of this
complementarity, all the information in the double-stranded sequence of a
DNA helix is duplicated on each strand, which is vital in DNA replication.
Indeed, this reversible and specific interaction between complementary base
pairs is critical for all the functions of DNA in living organisms.
Top, a GC base pair with three hydrogen bonds. Bottom, an AT base pair
with two hydrogen bonds. Non-covalent hydrogen bonds between the pairs
are shown as dashed lines.
The two types of base pairs form different numbers of hydrogen
bonds, AT forming two hydrogen bonds, and GC forming three hydrogen
29
bonds (see Figures). DNA with high GC-content is more stable than DNA
with low GC-content, but contrary to popular belief, this is not due to the
extra hydrogen bond of a GC base pair but rather the contribution of stacking
interactions (hydrogen bonding merely provides specificity of the pairing,
not stability) [16]. As a result, it is both the percentage of GC base pairs and
the overall length of a DNA double helix that determine the strength of the
association between the two strands of DNA. Long DNA helices with a high
GC content have stronger-interacting strands, while short helices with high
AT content have weaker-interacting strands [17]. In biology, parts of the
DNA double helix that need to separate easily, such as the TATAAT
Pribnow box in some promoters, tend to have a high AT content, making the
strands easier to pull apart [18]. In the laboratory, the strength of this
interaction can be measured by finding the temperature required to break the
hydrogen bonds, their melting temperature (also called Tm value). When all
the base pairs in a DNA double helix melt, the strands separate and exist in
solution as two entirely independent molecules [23]. These single-stranded
DNA molecules have no single common shape, but some conformations are
more stable than others.
DNA Structure
30
Components of DNA
Double stranded DNA has two strands
A phosphate-deoxyribose polymer composes the backbone of the DNA
Adjacent sugars are connected by phosphodiester bonds.
Nitrogenous bases are convalently bonded to the 1' carbon of the
deoxyribose.
The two DNA strands are antiparallel
The two strands are held together by hydrogen bonds between
complementary bases
Adenine hydrogen bonds (base pairs) to thymine
Guanine hydrogen bonds to cytosine
When DNA replicates two identical DNA double helices are formed
31
RNA Structure
A hairpin loop from a pre-mRNA.

Highlighted are the bases (light
green) and backbone (sky blue).
Ribonucleic acid (RNA) is a biologically important type of
molecule that consists of a long chain of nucleotide units. Each nucleotide
consists of a nitrogenous base, a ribose sugar, and a phosphate. RNA is very
similar to DNA, but differs in a few important structural details: in the cell,
RNA is usually single-stranded, while DNA is usually double-stranded;
RNA nucleotides contain ribose while DNA contains deoxyribose (a type of
ribose that lacks one oxygen atom); and RNA has the base uracil rather than
thymine that is present in DNA [17].
Chemical structure of RNA
32
An important structural feature of RNA that distinguishes it from
DNA is the presence of a hydroxyl group at the 2' position of the ribose
sugar. The presence of this functional group causes the helix to adopt the A-
form geometry rather than the B-form most commonly observed in DNA.
This results in a very deep and narrow major groove and a shallow and wide
minor groove [24].
1.1.7 Fatty acids and Lipids
Fatty Acids
The common fatty acids of plant tissues are C16 and C18 straight-
chain compounds with zero to three double bonds of a cis (or Z)
configuration. Such fatty acids are also abundant in animal tissues, together
with other even numbered components with a somewhat wider range of
chain-lengths and up to six cis double bonds separated by methylene groups
(methylene-interrupted) [26]. The systematic and trivial names of those fatty
acids encountered most often, together with their shorthand designations, are
listed in the table.
The common fatty acids of animal and plant origin
Systematic name Trivial name Saturated Shorthand

fatty acids
ethanoic acetic 2:0
butanoic butyric 4:0
hexanoic caproic 6:0
octanoic caprylic 8:0
decanoic capric 10:0
dodecanoic lauric 12:0
33
tetradecanoic myristic 14:0
hexadecanoic palmitic 16:0
octadecanoic stearic 18:0
eicosanoic arachidic 20:0
docosanoic behenic 22:0
Monoenoic fatty acids
cis-9-hexadecenoic palmitoleic 16:1(n-7)
cis-6-octadecenoic petroselinic 18:1(n-12)
cis-9-octadecenoic oleic 18:1(n-9)
cis-11-octadecenoic cis-vaccenic 18:1(n-7)
cis-13-docosenoic erucic 22:1(n-9)
cis-15-tetracosenoic nervonic 24:1(n-9)
Polyunsaturated fatty acids*
9,12-octadecadienoic linoleic 18:2(n-6)
6,9,12-octadecatrienoic γ-linolenic 18:3(n-6)
9,12,15-octadecatrienoic α-linolenic 18:3(n-3)
5,8,11,14-eicosatetraenoic arachidonic 20:4(n-6)
5,8,11,14,17-
EPA 20:5(n-3)
eicosapentaenoic
4,7,10,13,16,19-
DHA 22:6(n-3)
docosahexaenoic
* all the double bonds are of the cis configuration
34
The most abundant saturated fatty acid in
nature is hexadecanoic or palmitic acid. It can also be designated a "16:0"
fatty acid, the first numerals denoting the number of carbon atoms in the
aliphatic chain and the second, after the colon, denoting the number of
double bonds. All the even-numbered saturated fatty acids from C2 to C30
have been found in nature, but only the C14 to C18 homologues are likely to
be encountered in appreciable concentrations in glycerolipids, other than in a
restricted range of commercial fats and oils [27].
Oleic or cis-9-octadecenoic acid, the most abundant monoenoic fatty
acid in nature, is designated as "18:1", or more precisely as "18:1(n-9)", to
indicate that the last double bond is 9 carbon atoms from the terminal methyl
group.
The latter form of the nomenclature is of special value to

biochemists. Similarly, the most abundant cis monoenoic acids fall into the
same range of chain-lengths, i.e. 16:1(n-7) and 18:1(n-9), though 20:1 and
22:1 are abundant in fish. Fatty acids with double bonds of the trans (or E)
configuration are found occasionally in natural lipids, or are formed during
food processing (hydrogenation) and so enter the food chain, but they tend to
be minor components only of animal tissue lipids, other than of ruminants.
Their suitability for human nutrition is currently a controversial subject.
The C18 polyunsaturated fatty acids, linoleic or cis-9,cis-12-
octadecadienoic acid (18:2(n-6)) and α-linolenic or cis-9,cis-12,cis-15-
octadecatrienoic acid (18:3(n-3)), are major components of most plant lipids,
including many of the commercially important vegetable oils.
35
They are essential fatty acids in that they cannot be synthesised in
animal tissues. On the other hand, as linoleic acid is almost always present in
foods, it tends to be relatively abundant in animal tissues. In turn, these fatty
acids are the biosynthetic precursors in animal systems of C20 and C22
polyunsaturated fatty acids, with three to six double bonds, via sequential
desaturation and chain-elongation steps (desaturases in animal tissues can
only insert a double bond on the carboxyl side of an existing double bond).
Those fatty acids derived from linoleic acid, especially arachidonic acid
(20:4(n-6)), are important constituents of the membrane phospholipids in
mammalian tissues, and are also the precursors of the prostaglandins and
other eicosanoids [28]. In fish, linolenic acid is the more important essential
fatty acid, and polyunsaturated fatty acids of the (n-3) series, especially
eicosapentaenoic acid (20:5(n-3) or EPA) and docosahexaenoic acid (22:6(n-
3) or DHA), are found in greater abundance [24].
Many other fatty acids that are important for nutrition and health do
of course exist in nature, and at present there is great interest in γ-linolenic
acid (18:3(n-6)), the active constituent of evening primrose oil -
- and in conjugated linoleic acid (mainly, 9-cis,11-trans-octadecadienoate) or

'CLA', a natural constituent of dairy products, that is claimed to have
36
remarkable health-giving properties.
Branched-chain fatty acids are synthesised by many microorganisms (most

often with an iso- or an anteiso-methyl branch) and they are synthesised to a
limited extent in higher organisms [29]. They can also enter animal tissues
via the diet, especially those of ruminants.
Phytanic acid, 3,7,11,15-tetramethylhexadecanoic acid, is a

metabolite of phytol and is found in animal tissues, but generally at low
levels only.
Fatty acids with many other substituent groups are found in certain
plants and microorganisms, and they may be encountered in animal tissues,
which they enter via the food chain. These substituents include acetylenic
and conjugated double bonds, allenic groups, cyclopropane, cyclopropene,
cyclopentene and furan rings, and hydroxy-, epoxy- and keto-groups. For
example, 2-hydroxy fatty acids are synthesised in animal and plant tissues,
and are often major constituents of the sphingolipids [30] 12-Hydroxy-
octadec-9-enoic or 'ricinoleic' acid is the main constituent of castor oil.
37
- Lipids
Although lipid analyst tends to have a firm understanding of what is
meant by the term "lipid", there is no widely-accepted definition. General
text books usually describe lipids in woolly terms as a group of naturally
occurring compounds, which have in common a ready solubility in such
organic solvents as hydrocarbons, chloroform, benzene, ethers and alcohols.
They include a diverse range of compounds, like fatty acids and their
derivatives, carotenoids, terpenes, steroids and bile acids [31]. It should be
apparent that many of these compounds have little by way of structure or
function to relate them. In fact, a definition of this kind is positively
misleading, since many of the substances that are now widely regarded as
lipids may be almost as soluble in water as in organic solvents.
While the international bodies that usually decide such matters have
shirked the task, a more specific definition of lipids than one based simply
on solubility is necessary, and most scientist active in this field would
happily restrict the use of "lipid" to fatty acids and their naturally-occurring
derivatives (esters or amides). The definition could be stretched to include
compounds related closely to fatty acid derivatives through biosynthetic
pathways (e.g. prostanoids, aliphatic ethers or alcohols) or by their
biochemical or functional properties [22] (e.g. cholesterol)
“Lipids are fatty acids and their derivatives, and substances
related biosynthetically or functionally to these compounds.”
This treats cholesterol (and plant sterols) as a lipid, and could be
interpreted to include bile acids, tocopherols and certain other compounds. It
also enables classification of such compounds as gangliosides as lipids,
although they are more soluble in water than in organic solvents. However, it
does not include such natural substances as steroidal hormones, petroleum
products, some fat-soluble vitamins, carotenoids or simple terpenes, except
in rare circumstances [17].
38
If "lipids" are defined in this way, fatty acids must be defined also.
They are compounds synthesised in nature via condensation of malonyl
coenzyme. A unit by a fatty acid synthase complex. They usually contain
even numbers of carbon atoms in straight chains (commonly C14 to C24), and
may be saturated or unsaturated, and can contain a variety of substituent
groups.
Fahy et al. (J. Lipid Res., 46, 839-862 (2005)) have developed a
classification system for a lipid that holds promise [33]. While their
definition of a lipid is too broad for my taste, it is based on sound scientific
principles, i.e. Hydrophobic or amphipathic small molecules that may
originate entirely or in part by carbanion-based condensations of thioesters
(fatty acids, polyketides, etc.) and/or by carbocation-based condensations of
isoprene units [11].
The most common lipid classes in nature consist of fatty acids linked
by an ester bond to the trihydric alcohol - glycerol, or to other alcohols such
as cholesterol, or by amide bonds to sphingoid bases, or on occasion to other
amines. In addition, they may contain alkyl moieties other than fatty acids,
phosphoric acid, organic bases, carbohydrates and many more components,
which can be released by various hydrolytic procedures [14].
1.1.8 ADP and ATP
ATP (Adenosine Triphosphate)
Adenosine triphosphate (ATP) is considered by biologists to be the
energy currency of life. It is the high-energy molecule that stores the energy
we need to do just about everything we do. It is present in the cytoplasm and
nucleoplasm of every cell, and essentially all the physiological mechanisms
that require energy for operation obtain it directly from the stored ATP.
(Guyton) As food in the cells is gradually oxidized, the released energy is
used to re-form the ATP so that the cell always maintains a supply of this
essential molecule. Karp quotes an estimate that more than 2 x 1026
molecules or >160kg of ATP is formed in the human body daily! ATP is
39
remarkable for its ability to enter into many coupled reactions, both those to
food to extract energy and with the reactions in other physiological processes
to provide energy to them. In animal systems, the ATP is synthesized in the
tiny energy factories called mitochondria [35].
The structure of ATP has an ordered carbon compound as a backbone,

but the part that is really critical is the phosphorous part - the triphosphate.
Three phosphorous groups are connected by oxygens to each other, and there
are also side oxygens connected to the phosphorous atoms. Under the normal
conditions in the body, each of these oxygens has a negative charge, and as
you know, electrons want to be with protons - the negative charges repel
each other [36,37].These bunched up negative charges want to escape - to
get away from each other, so there is a lot of potential energy here.
If you remove just one of these phosphate groups from the end, so
that there are just two phosphate groups, the molecule is much happier. This
conversion from ATP to ADP is an extremely crucial reaction for the
supplying of energy for life processes. Just the cutting of one bond with the
accompanying rearrangement is sufficient to liberate about 7.3 kilocalories
per mole = 30.6 kJ/mol. Living things can use ATP like a battery. The ATP
can power needed reactions by losing one of its phosphorous groups to form
ADP, but you can use food energy in the mitochondria to convert the ADP
back to ATP so that the energy is again available to do needed work. In
plants, sunlight energy can be used to convert the less active compound
40
back to the highly energetic form. For animals, you use the energy from your
high energy storage molecules to do what you need to do to keep yourself
alive, and then you "recharge" them to put them back in the high energy
state.
Conversion from ATP to ADP
Adenosine triphosphate (ATP) is the energy currency of life and it
provides that energy for most biological processes by being converted to
ADP (adenosine diphosphate). Since the basic reaction involves a water
molecule,
ATP + H2O → ADP + Pi

this reaction is commonly referred to as the hydrolysis of ATP.
The structure of ATP has an ordered carbon compound as a backbone, but
the part that is really critical is the phosphorous part - the triphosphate.
If you remove just one of these phosphate groups from the end, so that there
are just two phosphate groups, the molecule is much happier. If you cut this
bond, the energy is sufficient to liberate about 7000 calories per mole, about
the same as the energy in a single peanut. Food molecules function as fuel
molecules, storing large quantities of energy in a stable form over long
41
periods of time. They are the long-term energy currency of the cell. Such a
molecule is adenosine triphosphate (ATP).
This molecule acts as the short-term energy currency of the cell and
provides the source of energy used in individual synthetic (nonspontaneous)
reactions. ATP collects small packets of energy from the food-burning
power plants of the cell and transports this energy to where it is needed.
Some energy in ATP is released to do work, such as move muscles or force a
seedling out of the ground. At other times, ATP gives up its energy to a
nonspontaneous synthetic reaction, such as the formation of sucrose [15].
When a molecule of fatty acid is burned, energy is given off. Some of
this energy is trapped in molecules of ATP, and some is lost in the form of
heat. Each ATP molecule can then be transported elsewhere within the
cell and used where needed.
Figure The ATP-ADP Cycle. Energy is needed for the formation of ATP and is
legend: released as the ATP is converted back to ADP and phosphate.
This cycle is used by cells as a means of converting the large amounts of energy
in food molecules into the smaller amounts of energy needed to drive the
synthetic reactions of cells, such as the formation of sucrose.
The energy-carrying part of an ATP molecule is the triphosphate "tail"
42
[38].Three phosphate groups are joined by covalent bonds. The electrons in
these bonds carry energy.
Within the power plants of the cell (mitochondria), energy is used to add one
molecule of inorganic phosphate (P) to a molecule of adenosine diphosphate
(ADP).
ADP + P + Energy ---> ATP
The amount of energy stored is about 7,300 calories for every mole of
ATP formed. At the energy-requiring site, the last phosphate group in the tail
is broken off and the energy in the bond liberated.
ATP --> ADP + P + Energy
Again, about 7,300 calories of energy per mole is released. The ADP
and the phosphate are then free to return to the power plant and be rejoined.
In this way, ATP and ADP are constantly being recycled.
Energy Storage
The processes of catabolism provide energy which must be made
available for performing useful work. The energy cannot be in the form of
heat because cells function at constant temperature. Heat energy is only
useful when transferred from a hot body to a cold body. The energy from
catabolism must be conserved or transformed into chemical storage. The
major chemical storage is in the form of adenosine triphosphate (ATP). ATP
is the link between exothermic reactions and endothermic reactions.
43
ATP is made of adenosine and ribose bonded to three phosphate
groups through phosphate ester bonds. ATP, ADP, AMP –
The importance of ATP centers on the storage of about 7 kcal/mole of
energy in the phosphorus-oxygen bond between the first and second
phosphate group [41]. The relationship of energy and the formation and
hydrolysis of ATP is illustrated in the following equations: P = PO4-3;
ADP = adenine diphosphate.
a) Hydrolysis: ATP + H2O --> ADP + P + energy
b) Formation: ADP + P + energy --> ATP + H2O
Under certain conditions ATP may be hydrolyzed directly to AMP (adenine
monophosphate).
ATP + H2O --> AMP + PP + energy
There are other metabolic phosphate molecules which store or give
off energy as needed. One further example is the hydrolysis of creatine
phosphate in muscle cells which also releases energy.
1.1.9 Hormones
Hormones are the chemical messengers of the body. They are defined
as organic substances secreted into blood stream to control the metabolic and
biological activities. These hormones are involved in transmission of
information from one tissue to another and from cell to cell. These
substances are produced in small amounts by various endocrine (ductless)
glands in the body. They are delivered directly to the blood in minute
quantities and are carried by the blood to various target organs where these
exert physiological effect and control metabolic activities. Thus frequently
their site of action is away from their origin. Hormones are required in trace
amounts and are highly specific in their functions. The deficiency of any
hormones leads to a particular disease, which can be cured by administration
of that hormone [22].
44
Classification of Hormones
Hormones are classified on the basis of (i) their structure (ii) their site of
activity in the cell.
Steroids on which the below classification is made are compounds
whose structure is based on four-ring network, consisting of 3 cyclohexane
rings and 1 cyclopentane ring.
Hypothalamus functions as master co-ordinator of hormonal action. It
produces atleast 6 releasing factors or hormones.
- Thyrotropin releasing hormone (TRH)
- Corticotropin releasing hormone (CRH)
- Gonadotropin releasing hormone (GnRH)
- Growth hormone releasing hormone (GRH)
- Growth hormone release inhibiting hormone (GRIH)
- Prolactin release inhibiting hormone (PRIH).
Functions of Steroid Hormones

- Sex hormones - are divided into 3 groups
(i) Female sex hormones or estrogens
(ii) Male sex hormones or androgens
(iii) Pregnancy hormones or progestines
Testosterone is the major male sex hormone produced by testes. It is
responsible for male characteristics (deep voice, facial hair, general physical
constitution) during puberty. Synthetic testosterone analogos are used in
45
medicine to promote muscle and tissue growth in patients with muscular
atrophy.
Progesterone is an example of progestin and is responsible for
preparing the uterus for implementation of the fertilized egg. It also has an
important role as birth control agents [28].
Functions of non steroid hormones
1. Peptide Hormones
Insulin has a profound influence or carbohydrate metabolism. It
facilitates entry of glucose and other sugars into the cells by increasing
penetration of cell membranes and augmenting phosphorylation of glucose.
This decreases glucose concentration in blood and insulin is commonly
known as hypoglycamic factor. It promotes anabolic processes and inhibits
catabolic ones. Its deficiency in human beings causes diabetes mellitus.
Insulin isolated from islets of Langerhens or islets tissue of pancreas was the
first hormone to be recognized as protein. Sanger determined the structure of
insulin and was awarded the Nobel prize in 1948 for this achievement.
2. Amino acid Derivatives
The thyroidal hormones e.g., thyroxin and tri-iodothyronine affect
the general metabolism, regardless of their specific activity. It is for this
reason why thyroid gland is known as pace setter of the endocrine system.
Based on the site of activity in the cell hormones are divided into two
categories first category of hormones effect the properties of plasma
membranes. These include all peptide hormones e.g., insulin and hormones
of pituitary gland.
1.1.10 Organometallic Biomolecules
Organometallic compounds have at least one carbon to metal bond,
according to most definitions. This bond can be either a direct carbon to
metal bond (σ bond or sigma bond) or a metal complex bond (π bond or pi
bond). Compounds containing metal to hydrogen bonds as well as some
46
compounds containing nonmetallic (metalloid) elements bonded to carbon
are sometimes included in this class of compounds. Some common
properties of organometallic compounds are relatively low melting points,
insolubility in water, solubility in ether and related solvents, toxicity,
oxidizability, and high reactivity [33].
An example of an organometallic compound of importance years ago
is tetraethyllead (Et44Pb) which is an antiknock agent for gasoline. It is
presently banned from use in the United States [18].
The first metal complex identified as an organometallic compound
was a salt, K(C2H4)PtCl3, obtained from reaction of ethylene with platinum
(II) chloride by William Zeise in 1825. It was not until much later (1951–
1952) that the correct structure of Zeise's compound was reported in
connection with the structure of a metallocene compound known as
ferrocene.
Preparation of ferrocene was reported at about the same time by two
research groups, and a sandwich structure was proposed, based on
ferrocene's physical properties (Kauffman, pp. 185–186). The sandwich
structure was confirmed by x-ray diffraction studies. Since then, other
metallocenes composed of other metals and other carbon ring molecules,
such as dibenzenechromium and uranocene have been prepared.
Possibly the first scientist to synthesize an organometallic compound
was Edward Frankland, who prepared diethylzinc by reaction of ethyl iodide
with zinc metal in 1849. 2 CH3CH2I + 2 Zn → CH3CH2ZnCH2CH3 + ZnI2
In organometallic compounds, most p-electrons of transition metals
conform to an empirical rule called the 18-electron rule. This rule assumes
that the metal atom accepts from its ligands the number of electrons needed
in order for it to attain the electronic configuration of the next noble gas. It
assumes that the valence shells of the metal atom will contain 18 electrons.
Thus, the sum of the number of d electrons plus the number of electrons
supplied by the ligands will be 18. Ferrocene, for example, has 6 d
47
electrons from Fe(II), plus 2 × 6 electrons from the two 5-membered rings,
for a total of 18. (There are exceptions to this rule, however.)
Possibly the earliest biomedical application of an organometallic
compound was the discovery, by Paul Ehrlich, of the organoarsenical
Salvarsan, the first antisyphilitic agent. Salvarsan and other organoarsenicals
are sometimes listed as organometallics even though arsenic is not a true
metal. Vitamin B12 is an organocobalt complex essential to the diet of human
beings. Absence of or deficiency of B12 in the diet (or a body's inability to
absorb it) is the cause of pernicious anemia.
Use as Reagents or Catalysts
Organometallic compounds are very useful as catalysts or reagents in
the synthesis of organic compounds, such as pharmaceutical products. One
of the major advantages of organometallic compounds, as compared with
organic or inorganic compounds, is their high reactivity. Reactions that
cannot be carried out with the usual types of organic reagents can sometimes
be easily carried out using one of a wide variety of available
organometallics. A second advantage is the high reaction selectivity that is
often achieved via the use of organometallic catalysts. For example, ordinary
free-radical polymerization of ethylene yields a waxy low-density
polyethylene, but use of a special organometallic catalyst produces a more
ordered linear polyethylene with a higher density, a higher melting point,
and a greater strength [41]. A third advantage is that many in this wide range
of compounds are stable, and many of these have found uses as medicinals
and pesticides. A fourth advantage is the case of recovery of pure metals.
Isolation of a pure sample of an organometallic compound containing a
desired metal can be readily accomplished, and the pure metal can then be
easily obtained from the compound. (This is generally done via preparation
of a pure metal carbonyl, such as Fe[CO]5 or Ni[CO]4, followed by thermal
decomposition.) Other commonly used organometallic compounds are
48
organolithium, organozinc, and organocuprates (sometimes called Gilman
reagents).
Grignard Reagents
One of the most commonly used classes of organometallic
compounds is the organomagnesium halides, or Grignard reagents (generally
RMgX or ArMgX, where R and Ar are alkyl and aryl groups, respectively,
and X is a halogen atom), used extensively in synthetic organic chemistry.
Organomagnesium halides were discovered by Philippe Barbier in 1899 and
subsequently developed by Victor Grignard.
1.2 Charge Transfer Interactions of Biomolecules and Inclusion
Compounds.
1.2.1 Organic Charge Transfer
A charge-transfer complex (or CT complex, electron-donor-
acceptor-complex) is a chemical association of two or more molecules, or of
different parts of one very large molecule, in which the attraction between
the molecules (or parts) is created by an electronic transition into an excited
electronic state, such that a fraction of electronic charge is transferred
between the molecules. The resulting electrostatic attraction provides a
stabilizing force for the molecular complex. The source molecule from
which the charge is transferred is called the electron donor and the receiving
molecule is called the electron acceptor, hence the alternate name, electron-
donor-acceptor-complex [42].
The nature of the attraction in a charge-transfer complex is not a
stable chemical bond and is much weaker than covalent forces; rather it is
better characterized as a weak electron resonance. As a result, the excitation
energy of this resonance occurs very frequently in the visible region of the
electro-magnetic spectrum. This produces the usually intense colors
characteristic for these complexes. These optical absorption bands are often
referred to as charge-transfer bands, or CT bands. Optical spectroscopy is a
powerful technique to characterize charge-transfer bands [43]. Charge-
49
transfer complexes exist in many types of molecules, inorganic as well as
organic, and in all phases of matter, i.e. in solids, liquids, and even gases.
In inorganic chemistry, most charge-transfer complexes involve
electron transfer between metal atoms and ligands. The charge-transfer
bands in transition metal complexes result from movement of electrons
between molecular orbitals (MO) that are predominantly metal in character
and those that are predominantly ligand in character. If the electron moves
from the MO with ligand like character to the metal like one, the complex is
called ligand-to-metal charge-transfer (LMCT) complex. If the electron
moves from the MO with metal like character to the ligand-like one, the
complex is called a metal-to-ligand charge-transfer (MLCT) complex. Thus,
a MLCT results in oxidation of the metal center whereas a LMCT results in
the reduction of the metal center [43]. Resonance Raman Spectroscopy is
also a powerful technique to assign and characterize charge transfer bands in
these complexes.
Donor-acceptor association equilibrium
Charge-transfer complexes are formed by weak association of
molecules or molecular subgroups, one acting as an electron donor and
another as an electron acceptor. The association does not constitute a strong
covalent bond and is subject to significant temperature, concentration, and
host (e.g., solvent) dependencies [44].
The charge-transfer association occurs in a chemical equilibrium
with the independent donor (D) and acceptor (A) molecules:
Quantum mechanically, this is described as a resonance between the

non-bonded state |D, A> and the dative state |D+...A->. The formation of the
dative state is an electronic transition giving rise to absorption bands [45].
The intensity of charge-transfer bands in the absorbance spectrum is
strongly dependent upon the degree (equilibrium constant) of this association
50
reaction. Methods have been developed to determine the equilibrium
constant for these complexes in solution by measuring the intensity of
absorption bands as a function of the concentration of donor and acceptor
components in solution. The methods were first described for the association
of iodine disolved in aromatic hydrocarbons [46].
Charge-Transfer transition energy
The color of charge-transfer bands, i.e., the charge-transfer transition
energy, is characteristic of the specific type of donor and acceptor entities.
The electron donating power of a donor molecule is measured by its
ionization potential which is the energy required to remove an electron from
the highest occupied molecular orbital [47]. The electron accepting power of
the electron acceptor is determined by its electron affinity which is the
energy released when filling the highest unoccupied molecular orbital.
The overall energy balance (ΔE) is the energy gained in a
spontaneous charge transfer. It is determined by the difference between the
acceptor's electron affinity (EA) and the donor's ionization potential (EI),
adjusted by the resulting electrostatic attraction (J) between donor and
acceptor:
The positioning of the characteristic CT bands in the electromagnetic

spectrum is directly related to this energy difference and the balance of
resonance contributions of non-bonded and dative states in the resonance
equilibrium.
Identification of CT bands
Charge transfer complexes are identified by -
Color: The color of CT complexes is reflective of the relative energy
balance resulting from the transfer of electronic charge from donor to
acceptor.
Solvatochromism: In solution, the transition energy and therefore the
51
complex color varies with variation in solvent permittivity, indicating
variations in shifts of electron density as a result of the transition. This
distinguishes it from the π→ π* transitions on the ligand.
Intensity: CT absorptions bands are intense and often lie in the ultraviolet or
visible portion of the spectrum. For inorganic complexes, the typical molar
absorptivities, ε, are about 50000 L mol-1 cm-1, that are three orders of
magnitude higher than typical ε of 20 L mol-1 cm-1 or lower, for d-d
transitions (transition from t2g to eg). This is because the CT transitions are
not spin or Laporte forbidden as d-d transitions.
Inorganic Charge-Transfer Complexes
Charge-transfer occurs often in inorganic ligand chemistry involving
metals. Depending on the direction of charge transfer they are either
classified as ligand-to-metal (LMCT) or metal-to-ligand (MLCT) charge-
transfer [48].
Charge Transfer Complexes and Color
Many metal complexes are colored due to d-d electronic transitions.
Visible light of the correct wavelength is absorbed, promoting a lower d-
electron to a higher excited state [49]. This absorption of light causes color,
although these colors are usually quite faint. This is because of two selection
rules:
The spin rule: Δ S = 0
On promotion, the electron should not experience a change in spin.
Electronic transitions which experience a change in spin are said to be spin
forbidden.
Laporte's rule: Δ I = ± 1
d-d transitions for complexes which have a center of symmetry are forbidden
- symmetry forbidden or Laporte forbidden [50].
Charge-transfer complexes do not experience d-d transitions. Thus, these
rules do not apply and the absorptions are generally very intense [51].
52
For example, the classic example of a charge-transfer complex is that
between iodine and starch to form an intense purple color.
1.2.2 Studies on charge transfer complexes.
Charge transfer complex between methylviologen and ferrocyanide
has been studied spectrophotometrically at different temperatures. From the
thermodynamic association constants (320 ± 30 M−1, 380 ± 30 M−1 and 460
± 40 M−1 at 15, 25 and 30°C respectively), the enthalpy of formation, ΔH° (−
3.4 ± 1.5 kcal/mole), and the related entropy change, ΔS°(0.4 ± 5 e.u), have
been calculated. The average extinction values of coefficients are 69±6 M−1
cm−1, 70±4 M−1 cm−1 and 72±5 M−1 cm−1 at 15, 25 and 35°C respectively
[52].
X-Ray crystal studies of the titled molecular complexes have
revealed the arrangement of parallel overlap between one of the benzene
rings of the heavily deformed TCNAQ moiety and donor benzene and
pyrene molecules, presumably attributable to the complex formation with
weak charge transfer interactions [53].
Iodine doping of C60 complexes with organic donors were carried
out. The solvent was gradually substituted by the iodine with the formation
of TPDP(C60)2I10, (TMDTDM-TTF)2C60I7.5, and DBTTFC60I9 compounds.
The doping results in strong changes in the donor electron state but only
indirectly affect the C60 electron system [54].
Novel electron acceptors, bithiazole analogues of
tetracyanodiphenoquinodimethane (TCNDQ), were synthesized by using a
Pd-catalyzed coupling reaction of a dibromated precursor with sodium
dicyanomethanide. The new acceptors show strong electron-accepting ability
and small on-site Coulomb repulsion [55].
A fluorometric method is used to study complexes between
thianthrene and various solvents including CCl4, CHCl3, acetone and
dichloroethane. Dichloromethane and dichloroethane are used as solvents
53
and systems are analyzed at 20 and 30°C.
Complex formation constants (Kf) determined in dichloroethane are
corrected for the solvent-thianthrene complex and are seen to be similar to
those determined in dichloromethane. The Stern-Volmer equation is shown
to be an incorrect choice in the analysis despite its yielding a linear plot. The
correct method yields a different value for Kf than does the Stern-Volmer
approach. Enthalpies of complex formation are also determined [56].
The visible and ultra-violet spectra of the charge-transfer complexes,
mesitylenechloranil, durene-chloranil and hexamethylbenzene-chloranil, in
carbon tetrachloride have been measured at 25°, 40°, 55° and 70°C. The
calculated values of equilibrium constants and maximum extinction
coefficients were found to be in disagreement with previous results. The
relationship between the equilibrium constant and the extinction coefficient
is discussed in terms of solvent interaction [57].
It was found that in halogen substitution reactions, bromine monochlonde
acts exclusively as a brominating agent. Formation of chloro-derivatives or
bromide ions could not be detected. Iodine monobromide, on the contrary,
proved to act partly as a lodinating, and partly as a brominating agent, even
in aqueous solutions containing bromide [58].
The complex formation of 1-ethyl-2-pyrrolidinone, 1-benzyl-2-
pyrrolidinone and 1-phenyl-2-pyrrolidinone with iodine, iodine
monobromide and iodine monochloride has been studied by u.v. and visible
spectroscopic methods in carbon tetrachloride, dichloromethane, 1,2-
dichloroethane, n-heptane and cyclohexane. The results show the
equilibrium constants (K), complexation enthalpies (ΔH) and the
wavelengths of maximum absorption bands (λmax) of the complexes to vary
markedly with the solvent. The decrease in the K values with increasing
acceptor number (AN) of the solvent may be due to the competition of the
solvent and the halogen molecule for the amide; for halogenated
hydrocarbon solvents can act as weak electron acceptors. The complex
54
formation ability of the electron donors decreases in the order 1-ethyl-2-
pyrrolidinone 1-benzyl-2-pyrrolidinone 1-phenyl-2-pyrrolidinone, and
the electron acceptor properties decrease in the order iodine monochloride
iodine monobromide iodine [59].
The formation of 1:1 hydrogen-bonded complexes of 2,2,2,-
trichloroethanol and 2,2,2-tribomoethanol with sulfoxides, sulfinamides,
sulfones and sulfonamides has been studied by i.r. spectroscopy in carbon
tetrachloride solution at 288.15, 298.15, 308.15 and 318.15 K. The
equilibrium constants have been measured from the change in intensity of
the free OH-stretching band of alcohols.
The results show that the equilibrium constants (K) and OH-
stretching wavenumber shifts (Δ OH) are in every case greater for the 2,2,2-
trichloroethanol complexes than for the corresponding 2,2,2-tribromoethanol
ones. Furthermore the proton acceptor strengths of sulfoxides and
sulfinamides seem to be of the same order of magnitude, as also the much
lower strengths of sulfones and sulfonamides, in agreement with earlier
suggestion that inductive effects predominate over resonance effects in
determining the polarity of sulfur-oxygen bonds in sulfinamides and
sulfonamides [60].
Complexes between various nitriles and ICl have been studied in
solution by infrared spectroscopic methods. The bond is directed from the
nitrogen to the iodine atom and is probably of the charge transfer type. The
infrared data indicate that in the case of acetonitrile the halogen molecule is
situated on the three-fold symmetry axis. Formation constants (Kc) of these
1:1 complexes in carbon tetrachloride at 28°C were obtained from intensity
changes of the C N stretching bands. The donor strength of the nitriles R-
C N is dependent upon the inductive effects of the substituent R. In the
complexes the C N stretching bands had higher frequencies (v), higher
integrated intensities (B) and generally larger half intensity widths (ν1/2) than
55
those of the free nitriles. Spectral parameters for these bands are given [61].
The vibrational spectra of the charge transfer complex of TTF with
TCNE are explored. It is found that a degree of charge transfer of 0.5,
namely that one electron has migrated from a dimer of TTF to that of TCNE
molecules, characterizes the ground state of the complex. A Holstein-
Hubbard model for a symmetric tetramer with two donor and two acceptor
molecules allows the understanding of the vibronic bands observed in the
infrared and Raman spectra and of the electronic charge transfer excitations
[62].
Charge Transfer (CT) absorption bands are observed in the
interaction of trialkytinhalides and TCNE. Taking account of Person's
restrictions the formation constants Kc of these complexes could be
accurately determined. A relation between the donor-acceptor separation,
rDA, and the size of the donor has been found. Arguments about the CT
absorption maximum, λCT, the formation constants and other spectral
evidence are in favour of the halide lone pairs as preferential donor site in
the organotiniodide molecule [63].
A spectro-photometric study on charge transfer complexes of
totrabromophthalic anhydride with various hydrocarbons has been made in
chloroform and benzene. In each case charge transfer bands characteristic of
the formation of 1 : 1 complexes have been observed. Equilibrium constant
Kc and extinction coefficient c for each of the complexes have been
calculated from the spectrophotometric data. Various predicted regularities
have been tested in the light of these results [64].
Charge transfer complex (CTC) of phenothiazine and iodine (1:2
molar ratio) was prepared by solvent evaporation method in diethyl ether and
its composite with poly(vinyl chloride) was prepared in benzene by diffusion
method. Infra-red spectra showed overlapped peaks for both components and
intensity of individual component was proportional to feed ratio. Optical
photographs and scanning electron microscopy of composites showed
56
template growth and connectivity in insulator matrix was proportional to
wt% of CTC. Mechanical strength of composites was found to increase with
wt% of PVC. The current–voltage study showed percolation threshold of
8 wt% of CTC. The temperature dependence of conductivity showed
semiconducting nature of the materials. Transport property of charges were
explained by regression analysis of σdc vs. T−1/1+n data and meets the basis for
the Mott's 2D, 3D variable range hopping or thermoionic emission model,
depending on temperature and wt% of CTC content. The impedance
spectroscopy was performed between 40 Hz–100 kHz range. Circuit
elements consists only combination of resistance and capacitance, which
showed homogeneous nature of composites. Thermoelectric factor ‘S’ was
also evaluated and has value of <1 at 303 K in all cases [65].
The intermolecular charge-transfer absorption spectra of complexes
of various p-π aromatic electron donor molecules with a series of p-π
aromatic electron acceptor molecules have been measured. The frequencies
of the bands of these complexes may be expressed simply as the sum of two
terms, characteristic of the donor and acceptor molecules respectively. This
relationship fails if the electron donor is weak [66].
A theory for charge transfer between the electrode and the
donor/acceptor molecule coupled through a DNA bridge in solution is
developed. They explore the crossover between the coherent tunneling and
the incoherent sequential transfer regimes by varying the electrode potential
and discuss the effects of single-base mismatches in DNA duplex in both
regimes. In the former regime a single-base mismatch in DNA duplex causes
a reduction in the charge transfer rate simply by decreasing the electron
tunneling matrix element, however, in the latter regime the effects are rather
complicated [67].
The intermolecular charge-transfer (CT) complexes formed between
two poly(amidoamine) dendrimers (PAMAM) from zero (D1) and second
generation (D2) as donor and iodine as σ-acceptor have been studied
57
spectrophotometrically in the chloroform medium. The suggested structures
of the solid iodine charge-transfer complexes investigated by several
techniques using elemental analysis, mid infrared spectra, and thermal
analysis (TGA and DTG) of the solid CT-complexes along with the
photometric titration curves for the reactions. The results indicate the
formation of two CT-complexes [(D1)]–I2 and [(D2)]–2I2 with acceptor:
donor molar ratios of 1:1 and 1:2, respectively. The kinetic parameters (non-
isothermal method) for their decomposition have been evaluated by
graphical methods using the equations of Horowitz–Metzger (HM) and
Coats–Redfern (CR) [68].
Weak interactions between organic donor and acceptor molecules
resulting in cofacially-stacked aggregates ("CT complexes") were studied by
second-order many-body perturbation theory (MP2) and by gradient-
corrected hybrid Hartree-Fock/density functional theory (B3LYP exchange-
correlation functional). The complexes consist of tetrathiafulvalene (TTF)
and related compounds and tetracyanoethylene (TCNE). Density functional
theory (DFT) and MP2 molecular equilibrium geometries of the component
structures are calculated by means of 6-31G*, 6-31G*(0.25), 6-31++G**, 6-
31++G(3df,2p) and 6-311G** basis sets. Reliable molecular geometries are
obtained for the donor and acceptor compounds considered. The geometries
of the compounds were kept frozen in optimizing aggregate structures with
respect to the intermolecular distance. The basis set superposition error
(BSSE) was considered (counterpoise correction). According to the DFT and
MP2 calculations laterally-displaced stacks are more stable than vertical
stacks. The charge transfer from the donor to the acceptor is small in the
ground state of the isolated complexes. The cp-corrected binding energies of
TTF/TCNE amount to -1.7 and -6.3 kcal/mol at the DFT(B3LYP) and
MP2(frozen) level of theory, respectively (6-31G* basis set). Larger binding
energies were obtained by Hobza's 6-31G*(0.25) basis set. The larger MP2
binding energies suggest that the dispersion energy is underestimated or
58
not considered by the B3LYP functional. The energy increases when S in
TTF/TCNE is replaced by O or NH but decreases with substitution by Se.
The charge-transferred complexes in the triplet state are favored in the
vertical arrangement. Self-consistent-reaction-field (SCRF) calculations
predicted a gain in binding energy with solvation for the ground-state
complex. The ground-state charge transfer between the components is
increased up to 0.8 e in polar solvents [69].
UV spectroscopy of charge-transfer complexes (CTCs) with
tetracyanoethylene (TCNE) and iodine has been used to study the relative
donor ability of mono- and bicycloolefins and the stability of the CTCs. The
donor ability of bicycloolefins, characterized by CT(TCNE), increases with
increase in ring strain. The equilibrium constants for complex formation of
bicycloolefins with TCNE are linearly related to the rate constants of the
reaction of epoxidation by tert-butyl hydroperoxide [70].
Charge transfer molecular complexes of some pyrazole donors
(pyrazole, 4-methylpyrazole, 3-methylpyrazole and 3,5-dimethylpyrazole)
with 2,3-dichloro-5,6-dicyano-1,4-p-benzoquinone and tetracyanoethylene
as π-electron acceptors have been studied in CH2Cl2 at 25 °C. Spectral
characteristics and stability constants of the formed charge transfer (CT)
complexes are discussed in terms of the nature of donor and acceptor
molecular structure, as well as in relation to solvent polarity.
Thermodynamic parameters (ΔH, ΔG and ΔS) associated with CT complex
formation are also examined. It was concluded that the formed CT
complexes are of n-π type with 1:1 (D:A) composition [71].
Charge transfer (CT) complexes formed between 2-amino-4-
methoxy-6-methyl-pyrimidine (AMMP), 2-amino-4,6-dimethyl-pyrimidine
(ADMP), 3-amino-pyrazole (AP), 3,5-dimethyl-pyrazole (DMP), 3-amino-5-
methyl-pyrazole (AMP), 2-amino-4-methyl-thiazole (AMT), 2-amino-5-
methyl-1,3,4-thiadiazole (AMTD) and 3-amino-5,6-dimethyl-1,2,4-triazine
(ADMT) as electron donors with the π-acceptor chloranilic acid (CHA)
59
were investigated spectrophotometrically in ethanol. Minimum–maximum
absorbances method has been used for estimating the formation constants of
the charge transfer reactions (KCT). It has been found that KCT depends on
the pKa of the studied donors. Job’s method of continuous variation and
photometric titration studies were used to detect the stoichiometric ratios of
the formed complexes and they showed that 1:1 complexes were produced.
The molar extinction coefficient (ε), oscillator strength (f), dipole moment
(μ), charge transfer energy (ECT), ionization potential (IP) and the
dissociation energy (W) of the formed complexes were estimated, they
reached acceptable values suggesting the stability of the formed CT-
complexes. The solid CT-complexes were synthesized and characterized by
elemental analyses, 1HNMR and FTIR spectroscopies where the formed
complexes included proton and electron transfer [72].
Molecular charge-transfer complexes of the donor 2,6-
diaminopyridine (2,6-DAPY) with π-acceptors tetracyanoethylene (TCNE),
2,3-dichloro-5,6-dicyano-p-benzoquinone (DDQ) and tetrachloro-p-
benzoquinone(chloranil) were studied spectrophotometrically in chloroform
at room temperature. All formed complexes exhibit well resolved charge-
transfer bands in the regions where neither donor nor acceptors have any
absorption. The stoichiometries of the reactions were determined from
photometric titration methods. The results obtained show the formed CT
complexes have the structures [(2,6-DAPY)(TCNE)3], [(2,6-
DAPY)(DDQ)2], and [(2,6-DAPY)(chloranil)]. These three complexes were
isolated as solids and further characterized by elemental analysis and
infrared measurements [73].
Poly(phenylethynyl)copper was prepared by reacting
phenylacetylene with Cu+ ions. Its dc conductivity drastically increases on
doping with iodine and 2,3-dichloro-5,6-dicyano-p-benzoquinone (DDQ).
An investigation using IR and UV spectroscopy, X-ray diffraction and solid
state NMR revealed that on iodine doping structural changes occur caused
60
by a reaction between Cu(I) and the dopant. On the contrary, on doping with
DDQ the structure is preserved. The large conductivity increase with the
latter dopant originates from charge transfer between the polymer chain
(donor) and DDQ (acceptor), evidenced by a transformation from a quinone
into a semiquinone structure of the DDQ molecule [74].
In present study synthesizing and characterizing organic conducting
materials have been focused primarily on the preparation and structure
determination of D-A-D (D = donor, A = acceptor) and A-D-A molecular
units in which donors and acceptors are chemically attached via bridging
atoms or groups. The strategy that motivates the synthetic work is aimed at
gaining control over the architectural features of the solid state structures of
the materials, since gaining control over the three-dimensional structure is a
vital pre-condition for achieving electrical conductivity in organic materials.
Construction of such molecular units predetermines the D-A molar ratio as
well as the maximum degree of charge transfer. Moreover, it is already
shown that this molecular motif has a high propensity to crystallize in the
desired crystallographic arrangement, characterized by segregated stacks of
both donors and/or acceptor, with significant overlap between adjacent units
in the stack. Following this approach we have synthesized two types of
molecules; have been synthesized one contains two donors attached to one
acceptor via -CH2- or S atom bridges, and in the other, two acceptors are
linked to one donor via methylene bridges.
In addition, the importance of introducing heavy atoms in charge-transfer
complexes has long been recognized. Consequently, extensive work has
been carried out on the synthesis of various TTF derivatives, in which Se and
Te atoms replace sulfur or hydrogen atoms in TTF. Recently, we have
synthesized new compounds in which two TTF molecules are linked via
tellurium atoms, are synthesized, e.g. TTF-Te-TTF and TTF-Te-Te-TTF,
and prepared their complexes with TCNQ. They all exhibit high conductivity
at room temperature [76].
61
Interaction of some thiazole and benzothiazole derivatives as donors
with certain di- and trinitrobenzene derivatives as acceptors results in the
formation of 1:1 molecular species. The infrared, NMR and ultraviolet
analysis of the complexes with non-acidic acceptors reveals the presence of
π-π* interaction from a HOMO of the thiazole nucleus or the phenyl moiety
of the benzothiazoles to a LUMO of the benzene ring of the acceptors. The
existence of this type of interaction is supported by HMO calculations on the
donor molecules. On the other hand, the molecular complexes derived from
acidic acceptors are stabilized, in addition to the π-π* interaction, by proton
transfer from the hydroxyl or carboxylic group of the acceptor to the amino
group of the aminothiazole donors. The ionization potentials of donors,
electron affinities of acceptors as well as the energy of the CT complexes
were computed from their u.v. and visible spectra [77].
Formation of the charge transfer complexes between benzo-15-
crown-5, dibenzo-18-crown-6, dibenzo-24-crown-8 and dibenzo-crown-10
and the π-acceptors DDQ and TCNE in dichloromethane solution was
investigated spectrophotometrically. The molar absorptivities and formation
constants of the resulting 1:1 molecular complexes were determined. The
stabilities of the complexes of both π-acceptors varies.All of the resulting
complexes were isolated in crystalline form and characterized. The
influences of potassium ion on the formation and stability of the TCNE
molecular complexes were studied. Effects of the crown ether structure and
the role of the K+ ion on the formation of charge transfer complexes are
discussed [78].
Interactions of diaza-18-crown-6 and diaza-15-crown-5, as electron
donors, with 2,3-dichloro-5,6-dicyano-1,4-benzoquinone (DDQ), as an
electron acceptor, have been investigated spectrophotometrically in
acetonitrile and chloroform solutions. The results indicated immediate
formation of an electron donor-electron acceptor complex
62
DA: which is followed by two relatively slow consecutive
reactions:
The pseudo-first-order rate constants for the formation of the ionic
intermediate and the final product have been evaluated at various
temperatures by computer fitting of the absorbance time data to appropriate
equations. The formation constants of the resulting DA complexes have also
been determined. The influences of both the azacrown’s structure and the
solvent properties on the formation of DA complexes and the rates of
subsequent reactions are discussed [79].
Various studies, such as spectrophotometry, solubility studies and
FT—NMR studies reveal that the interaction of dinitrobenzenes with
anilines is primarily due to charge transfer but in some cases, where very
concentrated solutions are involved, hydrogen bonding may dominate over
charge transfer.
The charge transfer complex (CT-complex) between oxatomide drug
and 2,3-dichloro-5,6-dicyanobenzoquinone (DDQ) was studied
spectrophotometrically in 10 solvents at different temperatures. The donor
oxatomide is found to form stable 1:1 stoichiometric complex with DDQ and
the stoichiometry was unaffected by change in polarity of the solvent
studied. The ΔH°, ΔS° and ΔG° values are all negative, so the studied
complex is reasonably stable and exothermic in nature. The ionization
potential of the drug was determined using the CT-absorption bands of the
complex in all the solvents. The dissociation energy of the charge transfer
excited state for the CT-complex in different solvents was also determined
and is found to be constant. The spectroscopic and thermodynamic
properties were observed to be sensitive to the nature of the solvent [80].
Charge-transfer complexes of some heteroaromatic N-oxides with
tetracyanoethylene, 2,3-dichloro-5, 6-dicyanobenzoquinone, tetrachlorocyclohexa-2,
5-diene-1,4-dione and 7,7,8,8-tetracyanoquinodimethane in methylene chloride were
63
investigated spectrophotometrically. The spectral data, molar extinction
coefficients and transition energies of the complexes formed as well as the
ionization potentials of the donors are reported. B -H and J
methods were applied to the determination of formation and apparent
formation constants, respectively. The effect of temperature and solvent on
the stability of the complexes are discussed [81].
1,4-Naphthalenediol gets converted to 1,4-naphthoquinone on
reaction with 1,4-benzoquinone. In the reaction, 1,4-benzenediol is formed.
The reaction passes through charge delocalisation in the equivalent keto and
enol forms. The spectroscopic and electrochemical studies discern the role of
equivalent charge transfer complex derived from 1,4-naphthoquinone with
1,4-benzenediol. The conversion of 1,4-naphthalenediol to 1,4-
naphthoquinone in the presence of oxidants such as hydrogen peroxide and t-
butylhydroperoxide are catalysed by 1,4-benzoquinone[82].
X-Benzylidenesanthranilic acid molecular complexes with π-
acceptors, tetracyanoethylene, 2,3-dichloro-5,6-dicyano-p-benzoquinone and
chloranil, have been studied. The intramolecular hydrogen bonding that
exists in such compounds greatly inhibits the transition of the nitrogen
azomethine n-electrons. The formation constant values and molar extinction
coefficients of the p-dimethyl-aminobenzylideneanthranilic acid-DDQ CT
complexes have been determined in CH2Cl2, C2H4Cl2 and CHCl3 in the
temperature range 10–30°C. Such CT complexes are of strong n-π type [83].
π-π Molecular complexes of [2.2.2] (1, 2, 4)- as well as 5, 15, 16-
trimethyl [2.2.2] (1, 2, 4) cyclophanes as electron donors with
tetracyanoethylene and 1,4-benzoquinones as acceptors have been studied
spectrophotometrically. The position of λmax of the longest wavelength
charge-transfer band in the visible spectra of the complexes has been used to
discuss the effect of the strain as well as the molecular structure in the tris-
bridged cyclophanes on their complexation with different π-acceptors. The
constitution and apparent formation constants of the molecular complexes
64
formed have been determined, and the effect of solvent on molecular
complexation has been discussed [84].
The interaction of iodine with triphenylamine, triphenylphosphine,
triphenylarsine and triphenystibine has been investigated by electronic
spectroscopy. Transformation of the outer charge-transfer complexes to the
inner complexes (quarternary salts) has been examined. The relations of the
ionization potentials of the donors with the hvc.t have been discussed and
various c.t. parameters have been estimated. Hydrogen bonding of these
donors with phenol have been reported [85].
Complexes of o-carboxyphenylhydrazoneacetoacetanilide
(o-CPHAA) with Cu(II), Ni(II) and Co(II) were studied in dioxane-water
using the Irving and Rossotti method over the temperature range 10–40 °C
and at constant ionic strength (0.1 M). The acid dissociation constant pKH1,2
of the ligand and the stepwise stability constants (log K1 and log K2) of the
complexes formed were computed at various temperatures. The values of the
stepwise and overall changes in ΔG, ΔH and ΔS accompanying the
neutralization of the ligand and complex formation were evaluated. This
study reveals that the ionization of the ligand in the mixed solvent is an
endothermic process, whereas the complex formation is an exothermic
reaction. The optimum conditions for complex formation and the
composition and stability constants (log K1) of the complexes formed in
solution between the ligand and Cu(II), Ni(II) and Co(II) were also
determined (spectrophotometrically) [86].
1.2.3. Earlier studies on charge transfer interactions of biomolecules.
The spectrophotometric and thermodynamic properties of different
substituted methylnaphthalenes charge transfer (CT) complexes with
tetracyanoethylene have been studied in carbon tetrachloride. The spectral
characteristics of the CT bands have also been discussed in relation to the
positions of methyl groups. The formation constants and the spectral
properties of the complexes are markedly affected with the substitution
65
position of the methyl groups. The ionization potentials of the donors are
determined [87].
Charge transfer (CT) complexes of some non-steroidal anti-
inflammatory drugs, naproxen and etodolac which are electron donors with
some π-acceptors, such as tetracyanoethylene (TCNE), 2,3-dichloro-5,6-
dicyano-p-benzoquinone (DDQ), p-chloranil (p-CHL), have been
investigated spectrophotometrically in chloroform at 21 °C. The coloured
products are measured spectrophotometrically at different wavelength
depending on the electronic transition between donors and acceptors. Beer's
law is obeyed and colours were produced in non-aqueous media. All
complexes were stable at least 2 h except for etodolac with DDQ stable for
5 min. The equilibrium constants of the CT complexes were determined by
the Benesi–Hildebrand equation. The thermodynamic parameters ΔH, ΔS,
ΔG° were calculated by Van’t Hoff equation. Stochiometries of the
complexes formed between donors and acceptors were defined by the Job's
method of the continuous variation and found in 1:1 complexation with
donor and acceptor at the maximum absorption bands in all cases [88].
The interactions of the electron donors 2-aminopyridine (2APY) and
3-aminopyridine (3APY) with the π-acceptors tetracyanoethylene (TCNE),
2,3-dichloro-5,6-dicyano-p-benzoquinone (DDQ), 2-chloro-1,3,5-
trinitrobenzene (picryl chloride, PC), and 2,3,5,6-tetrachloro-1,4-
benzoquinone (chloranil) were studied spectrophotometrically in chloroform
at room temperature. The electronic and infrared spectra of the formed
molecular charge transfer (CT) complexes were recorded. Photometric
titration showed that the stoichiometries of the reactions were fixed and
depended on the nature of both the donor and the acceptor. The molecular
structures of the CT-complexes were, however, independent of the position
of the amino group on the pyridine ring and were formulated as
[(APY)(TCNE)], [(APY)(DDQ)], [(APY)(PC)], and [(APY) (chloranil)].
The formation constants (KCT), charge transfer energy (ECT) and molar
66
extinction coefficients ( CT) of the formed CT-complexes were obtained
[89].
Charge transfer absorptions of linear oligosilanes and
silanorbornadienes, charge transfer induced oligomerization, polymerization
and cycloaddition of tetrasilacyclooctadiyne and its germanium analogues
are described. Photo-induced electron transfer reactions of various types of
organosilicon compounds are discussed in detail, and include photo-induced
chlorinative Si–Si bond cleavage, photo-induced nucleophilic Si–Si bond
cleavage, fluorinative Si–Si bond cleavage via electron transfer, skeletal
rearrangement via photo-induced electron transfer and the structure of a silyl
radical cation [90].
Charge transfer complexes (CTC) of 5,10,15,20-
tetraphenylporphyrin (TPP), 5,10,15,20-tetra(4-tolyl)porphyrin (TTP),
5,10,15,20-tetra(4-methoxyphenyl)porphyrin (TMP), Zn-5,10,15,20-
tetraphenylporphyrin (Zn-TPP), and Zn-5,10,15,20-tetra(4-tolyl)porphyrin
(Zn-TTP) with tetracyanoethylene (TCNE) have been studied at various
temperatures in CH2Cl2 and CCl4. The data are discussed in terms of
equilibrium constant (KCT), molar extinction coefficient ( CT),
thermodynamic standard reaction quantities (ΔG°, ΔH° and ΔS°), oscillator

strength (f), and transition dipole moment (μ). The spectrum obtained for
TPP/TCNE, TTP/TCNE, and TMP/TCNE systems shows two main
absorption bands at 475 and 690 nm, which are not due to the absorption of
any of the reactants. These bands are characteristic of an intermolecular
charge transfer involving the overlap of the lowest unoccupied molecular
orbital (LUMO) of the acceptor with the highest occupied molecular orbital
(HOMO) of the donor. The results reveal that the interaction between the
donors and acceptor is due to π–π* transitions by the formation of radical ion
pairs. The stoichiometry of the complexes was found to be 1:1 ratio by the
Job and straight line methods between donors and acceptor with the
maximum absorption bands at wavelengths of 475 and 690 nm. The
67
observed data show salvation effects on the spectral and thermodynamics
properties of CTC. The ionization potential of the donors and the
dissociation energy of the CTC were also determined and are found to be
constant [91].
Charge-transfer molecular complexes of 2-amino-5-X-1,3,4-
thiadiazole (D) (X = H, I; = CH3, II; = phenyl, III) with some π-electron
acceptors (A) have been studied in methanol. It is concluded that these
complexes are predominantly of the π-π type. Solid 1:1 CT complexes of the
donors I–III with π-acceptors DDQ and TCNE have been synthesized and
characterized [92].
The spectrophotometric and thermodynamic properties of different
substituted methylnaphthalenes charge transfer (CT) complexes with
tetracyanoethylene have been studied in carbon tetrachloride. The spectral
characteristics of the CT bands have also been discussed in relation to the
positions of methyl groups. The formation constants and the spectral
properties of the complexes are markedly affected with the substitution
position of the methyl groups. The ionization potentials of the donors are
determined [93].
Simple and sensitive spectrophotometric methods are described, for
the first time, for the determination of sodium salts of phenobarbital (1),
thiopental (2), methohexital (3) and phenytoin (4). The methods are based on
the reaction of these drugs as n-electron donors with the σ-acceptor iodine
and various π-acceptors: 7,7,8,8-tetracyanoquinodimethane; 2,3-dichloro-
5,6-dicyano-1,4-benzoquinone; 2,3,5,6-tetrachloro-1,4-benzoquinone;
2,3,5,6-tetrafluoro-1,4-benzoquinone; 2,5-dichloro-3,6-dihydroxy-1,4-
benzoquinone; tetracyanoethylene and 2,4,7-trinitro-9-fluorenon. Depending
on the solvent polarity, different coloured charge-transfer complexes and
radicals were developed. Different variables and parameters affecting the
reactions were studied and optimized. The formed complexes were examined
by UV/VIS, infrared and 1H-NMR. Due to the rapid development of
68
colours at ambient temperature, the obtained results were used on thin layer
chromatograms for the detection of the investigated compounds. Beer's plots
were obeyed in a general concentration range of 1–400 μg ml−1 for the
investigated compounds with different acceptors. Interference from some co-
formulated drugs was also studied [94].
The stoichiometry of charge transfer complexes formed between
Schiff base donors and aromatic hydrocarbon acceptors was established by
solid-liquid phase equilibrium diagram studies. The thermodynamic
functions of some stable charge transfer complexes were determined by
differential scanning calorimetry and the area under the curve of the
congruent compound is fixed as the criterion to predict the relative strength
of charge transfer complexes on the basis of thermodynamic parameters [95].
The electrical properties of bilayer lipid membranes modified with
strong electron acceptors are examined by the voltammetric method.
Diffusion-limited current-potential curves are obtained in the absence of
exogenous redox agents in the aqueous phase when the membrane is
modified with tetracyanoethylene (TCNE) or tetracyanoquinodimethane
(TCNQ). Other substituted 1,4-benzoquinone modifiers yield either no
response (chloranil) or a current-voltage response indicative of a membrane
limiting charge transfer step. In all cases that demonstrate an eletrical
response, material can be detected leaching into the aqueous phase by
spectroscopic means. Free radicals are detected subsequent to the mixing of
modifier with an organic phase containing lipid; however, the material
detected in the aqueous phase is not a radical [96].
Diaryl ditellurides as electron donors have interacted with bromine
and iodine as electron acceptors in chloroform to form 1: 1 molecular charge
transfer (CT) complexes, which absorb light at 540 and 670 nm,
respectively. The molar ratio methods were used to determine the ratios of
the CT complexes. Diphenyl, di-p-methoxy phenyl and di-p-ethoxy phenyl
ditellurides were reacted with DDQ in chloroform solutions and
69
immediately formed stable solid products which consisted of one molecule
of diaryl ditelluride and two molecules of DDQ. The complexes were
characterized by elemental analyses, IR, UV-visible and mass spectral data
[97].
The reactions of the electron donor 1-methylpiperidine (1MP) with
the π-acceptors 7,7,8,8-tetracyanoquinodimethane (TCNQ),
tetracyanoethylene (TCNE), 2,3-dichloro-5,6-dicyano-p-benzoquinone
(DDQ), 2,3,5,6-tetrachloro-1,4-benzoquinone (chloranil = CHL) and iodine
(I2) were studied spectrophotometrically in chloroform at room temperature.
The electronic and infrared spectra of the formed molecular charge-transfer
(CT) complexes were recorded. The obtained results showed that the
stoichiometries of the reactions are not fixed and depend on the nature of the
acceptor. Based on the obtained data, the formed charge-transfer complexes
were formulated as [(1MP)(TCNE)2], [(1MP)(DDQ)]·H2O, [(1MP)(CHL)]
and [(1MP)I]I3, while in the case of 1MP–TCNQ reaction, a short-lived CT
complex is formed followed by rapid N-substitution by TCNQ forming the
final reaction products 7,7,8-tricyano-8-piperidinylquinodimethane
(TCPQDM). The five solids products were isolated and have been
characterized by electronic spectra, infrared spectra, elemental analysis and
thermal analysis [98].
The molecular interactions between haloperidol and droperidol as
electron donors and each of iodine; 7,7,8,8-tetracyanoquinodimethane
(TCNQ); 2,3-dichloro-5,6-dicyano-1,4-benzoquinone (DDQ);
tetracyanoethylene (TCNE); 2,4,7-trinitro-9-fluorenon (TNF); and 2-3-5-6-
tetrabromo-1,4-benzoquinone (Bromanil) as acceptors have been
investigated spectrophotometrically. Different variables affecting the
reaction were studies and optimized. Beer's law was obeyed in a
concentration limit of 2.5–2500 μg ml−1 for the studied drugs with various
acceptors used. Electron affinities (EA) of the acceptors were found to
correlate with both the time required for maximum colour formation and
70
the molar absorptivities of haloperidol and droperidol. A Job's plot of the
absorbance versus the molar ratio of the drugs to iodine indicated 1:1 ratio
[99].
The reaction of ferric(III) acetylacetonate (donor), Fe(acac)3, with
iodine as a σ-acceptor and with other different π-acceptors have been studied
spectrophotometrically at room temperature in chloroform. The π-acceptors
used in this investigation are 2,3-dichloro-5,6-dicyano-1,4-benzoquinone
(DDQ), p-chloranil and 7,7′,8,8′-tetracyanoquinodimethane (TCNQ). The
results indicate the formation of 1:1 charge-transfer complexes with a
general formula, [Fe(acac)3 (acceptors)]. The iodine complex was shown to
contain the triiodide species, [Fe(acac)3]2I+I3−, based on the electronic
absorptions as well as on the Far-infrared absorption bands characteristic for
the non-linear triiodide species, I3−, with C2v symmetry. The proposed
structure of this complex is further supported by thermal and middle infrared
measurements [100].
One paper describes the preparation of an organic charge transfer
complex (CTC) based printable enzyme electrode. CTC crystals were
prepared by mixing TCNQ powder with TTF solution (in acetonitrile).
Glucose oxidase (GOD) was adsorbed at the CTC crystal surface in a
monolayer. A printable paste was prepared by mixing GOD-adsorbed
crystals with a binder and a solvent. This paste was applied to an electrode
cavity and vacuum dried. A thin layer of gelatin was cast on the paste filled
dried electrode, and cross-linked with glutaraldehyde in the dry condition.
The sensors were fixed in a flow injection system, and continuously
polarized at 0·15 V and 37°C, and the samples were automatically injected
every 30 min [101].
The interaction of pyrazolones as a donor with iodine as an acceptor
has been studied using spectrophotometric and constant activity methods.
The results indicate the formation of 1:1 molecular complex species ofn–σ*
type. The equilibrium constants of these complexes were determined at
71
different temperatures. The effect of nonpolar solvents are discussed in terms
of the solute–solute and solute–solvent competing equilibria. The
thermodynamic parameters were calculated [102].
Simple, rapid and sensitive spectrofluorimetric methods are
described, for the first time, for the determination of ciprofloxacin (CIP),
norfloxacin (NOR), pefloxacin (PEF) and fleroxacin (FLE). The methods are
based on the charge-transfer (CT) reaction of these drugs as n-electron
donors with 7,7,8,8-tetracyanoquinodimethane (TCNQ) as π-electron
acceptor. TCNQ was found to react with these drugs to produce intensely
transfer reaction complexes and the fluorescence intensity of the complexes
was enhanced in 21–35 fold higher than that of the studied fluoroquinolones
itself. The formation of such complexes was also confirmed by both infrared
and ultraviolet-visible measurements. The different experimental parameters
that affect the fluorescence intensity were carefully studied. At the optimum
reaction conditions, the drug-TCNQ complexes showed excitation maxima
ranging from 277 to 284 nm and emission maxima ranging from 451 to
458 nm. Rectilinear calibration graphs were obtained in the concentration
range of 0.03–0.9, 0.04–1.2, 0.04–1.3 and 0.08–2.4 μg ml−1 for CIP, NOR,
PEF and FLE, respectively [103].
Heterogeneous electron transfer (ET) reactions at the polarised water
1,2-dichloroethane (DCE) interface are studied by in situ UV-Visible
spectroscopy in total internal reflection mode. The reduction of
7,7,8,8-tetracyanoquinodimethane (TCNQ) and the oxidation of
1,1′-dimethylferrocene (DMFc) by the hexacyanoferrate redox couple are
considered. The generation of products in the organic phase is monitored
spectroscopically and correlated to the simultaneous current response. Both
systems exhibit a good correlation between optical and electrochemical
responses, highlighting the ideal behaviour of these redox couples for
electron transfer studies at liquid liquid interfaces. The kinetics of ET
between hexacyanoferrate and TCNQ is analysed also by
72
chronoabsorptometry and potential modulated reflectance spectroscopy
[104].
Copper(II) and nickel(II) biguanides and O-alkyl-1-amidinourea can
act as donors for the formation of charge transfer (CT) adducts with I2 and
tetracyanoquinodimethane (TCNQ) as acceptors. Iodine adducts are
characterized both in solid and solution states whereas TCNQ adducts obtain
only in solution. Appearance of a broad band at 355 nm for iodine adducts
and at 335 nm for TCNQ adducts and shifting of i.r. frequencies support the
formation of donor acceptor associates. Elemental analysis establishes 1:1
stoichiometry of the solid adducts. The K and values determined by
modified Benesi—Hildebrand, Scott and Rose—Drago equations are found
to be of the order of 104 and 103 respectively at 298 K in methanol. The
solvent effect on the K values is discussed in terms of coupled solute-solute
and solute-solvent equilibria [105].
The charge-transfer complex formation of iodine with antipyrine has
been studied spectrophotometrically in chloroform, dichloromethane (DCM)
and 1,2-dichloroethane (DCE) solutions at 25 °C. The results indicate the
formation of 1:1 charge-transfer complexes. The observed time dependence
of the charge-transfer band and subsequent formation of I3− in solution were
related to the slow transformation of the initially formed 1:1 antipyrine:I2
outer complex to an inner electron donor–acceptor (EDA) complex, followed
by fast reaction of the inner complex with iodine to form a triiodide ion. The
values of the equilibrium constant, K, are calculated for each complex and
the influence of the solvent properties on the formation of EDA complexes
and the rates of subsequent reaction is evaluated [106].
The spectral properties of molecular complexes between some [2.2]
paracyclophane-azomethines and both tetracyanoethylene and 1,4-
benzoquinones in methylene chloride have been examined. The probability
of existence of the electronic transanular substituent effect in the
[2.2]paracyclophane-azomethines, as well as the effect of the different
73
substituted aryl groups on complexation have been discussed. The
stoichiometry, transition energy and apparent formation constants of the
molecular complexes formed have been determined spectrophotometrically
[107].
Charge-transfer molecular complexes of 2-amino-5-X-1,3,4-
thiadiazole (D) (X = H, I; = CH3, II; = phenyl, III) with some π-electron
acceptors (A) have been studied in methanol. It is concluded that these
complexes are predominantly of the π-π type. Solid 1:1 CT complexes of the
donors I–III with π-acceptors DDQ and TCNE have been synthesized and
characterized [108].
Spectrophotometric studies on the charge transfer interaction of 2,3
dichloro 5,6 dicyano p-benzoquinone with various hydrocarbons have been
carried out in chloroform. It has been observed that the frequency of the
charge transfer band at its maximum varies almost linearly with the
ionization potential of the donor. The singlet—triplet transition of some of
hydrocarbons has been bound to be coincident with the charge transfer
bands. Charge transfer spectra of all the systems studied are given and from
it λmax max and kc, have been determined [109].
EPR spectra of cobalt (II) complexes of octaethylporphyrin and
tetraphenylporphyrin, CoOEP and CoTPP, are strongly affected by
interactions with π electron donors or acceptors, the effects of the interaction
being generally larger in CoOEP than in CoTPP. Much smaller but still
significant effects of charge transfer complex formations were observed also
on EPR and ENDOR spectra of copper (II) porphyrins, CuOEP and CuTPP.
Direct charge transfer interactions between the metal d orbitals and the π
donors or acceptors make important contributions to the perturbation of the
metal d orbital states by the charge transfer complex formation [110].
Previously it has has been shawned that when glucocorticoids
initially enter rat thymus cells incubated at 37°C. Non-activated hormone-
receptor complexes are formed within 15 s and are then rapidly replaced
74
by activated complexes. Activated and non-activated forms were identified
in cytosols from the cells by DEAE-cellulose chromatography, where they
are eluted with progressively higher salt concentrations in what are referred
to as Peaks I and II [111].
On DNA-cellulose columns dexamethasone-receptor complexes in
cytosols that on DEAE-cellulose give mainly Peak II (the non-activated
complex, referred to as Complex II) are not bound significantly: they are
eluted at the lowest salt concentration along with free steroid, from which
they can be separated by binding to hydroxyapatite. This DNA-cellulose
peak is referred to as Peak a. Complexes in cytosols that give only Peak I on
DEAE, however, on DNA separate into two components. One of these
(Complex Ia) is not bound significantly and appears in Peak a. The other
(Complex Ib, presumably the true activated complex) appears in a later Peak
b. These three complexes have been measured by first adsorbing Ib with
DNA-cellulose, then separating Complexes Ia and II. Which are not
adsorbed on DNA. by means of a DEAE-cellulose column. When
[3H]-dexamethasone is added to cells at 37°C. II is formed within 15 s and is
rapidly replaced by Ib, in agreement with earlier results [112].
1.2.4 Recent studies on charge transfer Interactions of biomolecules
Cloxacillin sodium has been shown to form charge transfer (CT)
complexes of 1:1 stoichiometry with a number of electron acceptors in 50%
(v/v) aqueous ethanol medium. From the trends in the CT absorption bands,
the vertical ionization potential of the drug molecule (cloxacillin sodium) has
been estimated to be 7.89 eV. The enthalpies and entropies of formation of
two such complexes have been determined by estimating the formation
constants spectrophotometrically at five different temperatures. The
oscillator strengths and transition dipole moments of these complexes have
been determined. It has further been noted that the reduction of o-chloranil
by aqueous ethanol is completely inhibited by cloxacillin sodium, a
75
phenomenon that makes the present study of formation equilibrium possible
[113].
Charge transfer complexes between colchicine as donor and
π acceptors such as tetracyanoethylene (TCNE), 2,3-dichloro-5,6-dicyano-
p-benzoquinone (DDQ), p-chloranil (p-CHL) have been studied
spectrophotometrically in dichloromethane at 21 °C. The stoichiometry of
the complexes was found to be 1:1 ratio by the Job method between donor
and acceptors with the maximum absorption band at a wavelength of 535,
585 and 515 nm. The equilibrium constant and thermodynamic parameters
of the complexes were determined by Benesi–Hildebrand and van’t Hoff
equations. Colchicine in pure form and in dosage form was applied in this
study. The formation constants for the complexes were shown to be
dependent on the structure of the electron acceptors used [114].
A (2) catenane consisting of a π-electron-accepting tetracationic
cyclophane of cyclobis (4,4′-azopyridinium-p-phenylene) and a π-electron-
donating macrocyclic polyether of bis-p-phenylene-34-crown-10 was
synthesized via a template-directed synthesis in 68% yield. The (2) catenane
exhibited charge transfer bands with λmax=526 nm and 566 nm in CH3CN. A
precursor of the cyclophane, bis[4-(4-pyridylazo)pyridinium], spontaneously
formed a charge transfer complex with the macrocyclic polyether. The
investigation of the charge transfer complex using UV-visible and 1H NMR
spectroscopy revealed that the complex had a pseudo-rotaxane structure with
a stability constant (Ka) of 120 dm3 mol-1 at 25°C in CH3CN [115].
Spectrophotometric studies of several substituted benzanilides as
electron donors with tetracyanoethylene (TCNE) and 2,3-dichloro-5,
6-dicyanobenzoquinone (DDQ) as electron acceptors have given results that
are consistent with an interpretation of 1:1 charge-transfer (CT) complexes.
The nature of interaction as well as the substituent effects on the CT
complexation are discussed [116].
76
The charge-transfer (CT) interactions of thiophene, furan, pyrrole
and N-methylpyrrole with tetracyanoethylene, chloranil and maleic
anhydride have been investigated by electronic spectroscopy. In some cases
two CT bands were observed. The association constants of these CT
complexes were compared with those of the H-bonding of these
heterocyclics with phenol [117].
The d.c. electrical properties of polycarbonate (PC) in the dark and
their modification by some charge-transfer (CT) complexes were
investigated. The CT complexes were formed between two low-molecular-
weight additives, trans-stilbene and tetracyanoethylene (TCNE) and between
TCNE and the polymer. The time dependence of current after applying or
removing a step voltage was investigated in the temperature range 77–370 K.
At higher temperatures (above 330 K), three components of the current,
which differ in time and voltage dependence, were distinguished. Their
possible origin is discussed. The conduction current, which is measurable
above room temperature, is increased only slightly by the investigated CT
complexes, in spite of their strong influence on the photoconductivity of PC.
It is concluded that the electrical properties of these systems in the dark are
dominated by the polymer matrix, and that the additives take part in the
photogeneration process, but contribute to the transport of the charge carriers
to only a small extent [118].
Errors and misconceptions arising from Mulliken's treatment of
π-molecular complexes are discussed. Attention is drawn to the common
misuse of the term charge-transfer complex to describe complexes in which
the importance of charge transfer forces has not been established. It is
pointed out that information concerning the importance of charge transfer
forces can best be obtained from measurements of stability constants of
complexes formed by unsubstituted aromatic hydrocarbons. Measurements
of this kind are reported for the complexes formed by fourteen such
77
hydrocarbons with TCNE (tetracyanoethylene). The results do not indicate
any major contribution to binding by charge-transfer forces [119].
The charge-transfer complex formation between an electron donor
polymer, namely poly(2-vinyl pyridine) and low molecular weight acceptors
namely 7,7′,8,8′-tetracyanoquinodimethane and iodine has been investigated
by measuring electronic absorption spectra in dichloroethane at 25°C. The
formation of charge-transfer complexes of 2-picoline with the same set of
acceptors has also been studied as models for comparison. An alternative
method has been proposed to determine the molar ratio and equilibrium
constant for charge-transfer complex formation by electronic spectroscopy.
The equilibrium constant and molar absorptivity for the polymeric
complexes are found to be higher than those for the analogous model
complexes. The charge-transfer complexes undergo an irreversible reaction
to give a final product. The charge-transfer complexes have been studied by
electron spin resonance spectra [120].
Ultraviolet—visible spectral data of iodine complexes of n- and
π-donors have been interpreted by considering that the repulsion energy
responsible for the blue shift of the iodine band is also experienced by the
donor partner which causes the blue shift of the original band of the donor.
This reasoning explains the spectral data of iodine complexes of benzene,
pyridine-N-oxide and stilbazoles. Ultraviolet—vis. spectra of the iodine
complexes of pyridine, aminopyridines and diazines have been
reinvestigated and discussed in the light of the above reasoning. The above
reasoning is extended to the CT spectra of iodine complexes of twin-site
donors such as 1,10-phenanthroline, its methyl and chloro derivatives,
1,7 and 4,7-phenanthrolines, 2,2′-bipyridine and 4,4′-bipyridine. Arguments
are presented which indicate that the donors used in this study form only 1:1
complexes with iodine. The thermodynamic parameters were evaluated for
iodine complexes of the above twin-site donors. The kinetics of
78
transformation of outer CT complexes between the donors and iodine to
inner complexes is presented and discussed [121].
One subject review drawn attention to the peculiarities in behaviour
of bands in the electronic absorption spectra of electron donor–iodine–
solvent systems, the appearance of which is associated with the
intermolecular interaction of molecular iodine with electron donor organic
molecules. The new concept of the bands’ attribution to the isomeric
equilibrium molecular charge-transfer complexes (CTCs) of CTC-I and
CTC-II types is considered. The features of possible phase transitions in the
solid state are discussed on the basis of the thermodynamic properties and
electronic structures of the CTC-I and CTC-II in electron donor–iodine–
solvent systems. The stabilisation of the CTC-II structure with the
temperature lowering coincided in many cases with the electrons’
localisation in the solid state structures having charge-transfer bonds [122].
Spectrophotometric procedures are presented for the determination
of two commonly used antidepressant drugs, fluoxetine (I) and sertraline
hydrochloride (II). The methods are based mainly on charge transfer
complexation reaction of these drugs with either π acceptors chloranil and 2,
3 dichloro-5, 6-dicyanoquinone (DDQ) or σ acceptor iodine. The colored
products are quantified spectrophotometrically at 550, 450 and 263 nm for
fluoxetine and at 450, 455 and 290 nm for sertraline in chloranil, DDQ and
iodine methods, respectively. The molar combining ratio and the optimum
assay conditions were studied. The methods determine the cited drugs in
concentration ranges of 80–640, 16–112 and 7.5–60 μg/ml with mean
percentage recoveries of 99.83, 99.76 and 100.00% and R.S.D. of 1.24, 0.95
and 1.13% in fluoxetine and ranges of 16–160, 15–105 and 6–48 μg/ml with
mean percentage recoveries of 100.39, 99.78 and 99.69% and R.S.D. of 1.02,
0.81 and 0.57% in sertraline for chloranil, DDQ and iodine methods,
respectively [123].
79
Charge transfer (CT) interaction of polyphenylacetylene (PPA) with
iodine, arsenic pentafluoride and 2,3-dichloro-5,6-dicyano-p-benzoquinone
(DDQ) in solution is associated with the formation of broad CT bands
extending beyond the absorption edge of the polymer into the near infra-red
and with a substantial loss of the polymer's effective conjugation. For PPA-I2
and PPA-DDQ in dilute solutions and at low doping levels, the 1:1 CT
complex is susceptible to a Benesi-Hildebrand analysis. The microstructure
of the polymer has a pronounced effect on the observed interaction rates and
equilibrium constants. At high acceptor loadings, there are complicated time-
dependent equilibria involving several complexes of different stoichiometry.
The role of the CT state in this electroactive polymer is discussed in the
context of a band-like model [124].
The charge-transfer interactions between the electron donor 4,
4′-trimethylenedipiperidine (TMDP) and the acceptors 2,3,5,6-tetrachloro-
1,4-benzoquinone (chloranil), 2,4,4,6-tetrabromo-2,5-cyclohexadienone
(TBCHD), 2,3-dichloro-5,6-dicyano-1,4-benzoquinone (DDQ),
7,7′,8,8′-tetracyanoquinodimethane (TCNQ) and iodine have been studied
spectrophotometrically in CHCI3 solutions. The formed solid charge-transfer
complexes were also isolated and characterized through infrared spectra as
well as thermal and elemental analysis. The stoichiometry of the complexes
was found to be 1:1 in the case of TMDP–chloranil and TMDP–TBCHD
systems and 1:2 in the case of TMDP–DDQ and TMDP–TCNQ systems and
1:3 in the case of TMDP–iodine system. Taking this into consideration along
with infrared spectra and thermal and elemental analysis, the formed
CT complexes have the formulas [(TMDP)(chloranil)], [(TMDP)(TBCHD)],
[(TMDP)(DDQ)2] [(TMDP)(TCNQ)2] and [(TMDP)I]+·I5−, respectively
[125].
The charge transfer donor (D)–acceptor (A) complexes formed
between three classes of vitamin K (all electron acceptors in this study) with
several thiazine psychotropes, used also as antimicrobials, antimalarials,
80
antibiotics, and anticoagulants, were studied by means of alternating current
titrations. The monochloride thiazines formed 2:1 (D:A) complexes,
interacting from 26 to 47.5%; the dihydrochloride formed a 3:1 (D:A)
complex. The antimalarials quinine and its isomer quinidine yielded 2:1
(D:A) complexes, interacting 51 and 60%, respectively. Quinacrine did not
complex with vitamin K. The antibiotics sulfisoxasole and sulfamethisole
gave 1:1 complexes, respectively interacting 6.2 and 11.7% [126].
The electrical properties of some charge transfer complexes, with
stoichiometries 1:1 and 1:2 (donor : acceptor), of 1,5-diaminonaphthalene
and 2,3-diaminonaphthalene with dinitro- and trinitrobenzenes have been
investigated. The positive temperature coefficient of electrical conductivity
(dσ/dT) is evidence for a semiconducting character. The energy gaps (Eg) for
conduction and the charge transfer excitation energies (ECT) have been
discussed. The mechanism of the conduction process is also interpreted
[127].
Inspection of the chemical structure of various drugs suggests that
they might interfere with thyroid metabolism by complexing molecular
iodine in the thyroid gland. Spectroscopic analysis shows that such
compounds form charge transfer complexes with iodine in a 1:1
stoichiometry. Strong donor-acceptor interactions were indicated by the high
values of formation constant Kc for the iodine/drug complexes [128].
The new charge transfer complex t-TTF-TCNQ, whose unsymmetric
cation is intermediate between TTF and HMTTF, presents a regular stacking
of both donor and acceptor chains. They showed that this compound had a
metallic behavior at high temperatures and underwent one metal-insulator
transition near 81 K. Its electrical and magnetic properties are examined in
connection to this phase transition and the effective dimensionality [129].
The iodine charge transfer complexes of thiazole, 4-methylthiazole,
2,4-dimethylthiazole, and benzothiazole in carbon tetrachloride have been
studied by the constant activity method. The equilibrium characteristics of
81
the CT complexes formed were measured. It was concluded that the CT
complexes are of the n-σ* nature and the donating site for the charge transfer
interaction is the lone pair of electrons on the nitrogen atom. Moreover, the
effect of substitution on the CT equilibrium was also studied. The
equilibrium constants have been found to be satisfactorily correlated with the
pK values of the respective thiazole derivatives. This can be attributed to the
lone pair of electrons on nitrogen being more localized on increasing the
donating power of substituent. Hence, the electron density on the nitrogen
atom increases and an increase in equilibrium constant was seen [130].
The solid charge-transfer (CT) complexes of some anthracene
derivatives with nitroaromatic acceptors were prepared. The ionization
potential IP, electron affinity EA and energy of the CT transition for the
donors, acceptors and CT complexes respectively were determined from the
spectrophotometric measurements. In addition, the electrical properties of
the CT complexes were investigated. The positive temperature coefficient of
electrical conductivity (dσ/dT) found for all samples provides evidence of
their semiconducting properties. A correlation between the
spectrophotometric and conductivity parameters was established. The
mechanism of the conduction process in these complexes was also studied
[131].
Charge transfer complexes between iodine and
hexamethylphosphoramide chalcogenides have been investigated
spectrophotometrically. The equilibrium constant increases on passing from
O to Se but not proportionally to the ionization potential of the atoms. A
linear correlation was found between ΔG (or ΔS) and ΔH. The structure of
the complexes is discussed [132].
The interactions of iodine with oxidized cholesterol,
dipalmitoyllecithin and egg lecithin were studied by the monolayer method.
It was found that iodine is incorporated in the hydrophobic region of the
film, unsaturated bonds being essential for the process. No interaction
82
with hydrophilic groups could be detected. The iodide ion had no effect on
the incorporation. The amount of incorporated iodine was the largest for egg
lecithin, and less for oxidized cholesterol, while dipalmitoyllecithin showed
no measurable effect. This tendency is in accordance with the charge-transfer
complexing abilities of the lipids and the effect of iodine on the conduction
of hydrated lipid samples. Our results thus favour the electronic conduction
mechanism in iodine-doped bilayer systems [133].
The naphthoquinone acceptors form stable charge-transfer
complexes in solutions of aprotic solvents with aromatic hydrocarbons as
donors. From the charge-transfer transition energies of the complexes as well
as from the polarographic half-wave reduction potentials of the acceptors
relative electron affinities of the acceptors are determined. In addition, the
association constant, molar extinction coefficients, oscillator strengths, and
enthalpies of formation of the complexes were obtained from charge-transfer
spectral studies with hexamethylbenzene as donor. The average electron
affinities of 2,3-dichloro-(0·90 eV), 2,3-dichloro-5-nitro-(1·18 eV),
2,3,5,6-tetrachloro-7-nitro-(1·30 eV), 2,3-dicyano-(1·53 eV), 2,3-dicyano-
5-nitro-(1·68 eV), and 2,3-dicyano-5,6-dichloro-7-nitro-1,4-naphthoquinone
(1·75 eV) obtained from the charge-transfer spectral studies clearly show the
cumulative effects of electron-withdrawing substituents on the
naphthoquinone -system [134].
Quantum mechanical calculations show that azidopentazole forms
charge transfer complexes with benzene as well as with nitrobenzene. With
the former it reacts as an electron acceptor whereas with nitrobenzene it
functions as an electron donor. The stabilization energy in both cases was
found to be 4.5 kcal/mol [135].
Charge transfer (CT) complexes formed between 2-amino-
1,3,4-thiadiazole as donor and 2,3-dichloro-5,6-dicyano-p-benzoquinone
(DDQ), p-chloranil (p-CHL), o-chloranil (o-CHL), p-bromanil (BRL) and
chloranilic acid (CHA) as acceptors, have been studied
83
spectrophotometrically. Benesi-Hildebrand and Job continuous variation
methods were applied to the determination of association constant (K), molar
extinction coefficients ( ), dipole moment and stoichiometric ratio,
respectively. The solid CT complexes have been synthesized and
characterized by different spectral methods. The spectral changes reveal that
the CT interaction depends on the type of the acceptors. The magnetic
properties of the various complexes were also investigated. The electrical
properties for the solid CT complexes are measured from which the
activation energies are calculated [136].
In the present study CT complexes of 2-, 3- and 4-Picolines with
(DDQ) 2, 3-dichloro-5, 6-dicyano parabenzoquinone (π-acceptor) and (I2)
Iodine (σ-acceptor) have been investigated spectrophotometrically in three
different solvents (CCl4, CHCl3 and CH2Cl2) at six different temperatures.
The formation constants of the CT complexes were determined by the
Benesi-Hildebrand equation. The thermodynamic parameters were calculated
by Van’t Hoff equation. The ΔH°, ΔG° and ΔS° values are all negative
implying that the formation of studied complexes is exothermic in nature
[137].
Charge transfer complexes of substituted-N-aryl-N-4-(-p-anisyl-
5-arylazothiazolyl)thiourea with 2,3-dichloro-5,6-dicyanobenzoquinones
(DDQ), chloranilic acid (CHLA), chloranil (CHL), bromanil (BRL) and
iodanil (IDL) in methylene chloride were investigated
spectrophotometrically to determine association constants (K), molar
extinction coefficients (ε) and stoichiometric ratio. The effect of
thermodynamic parameters (ΔG* and ΔH) on the stability of the complexes
are discussed and the transition energy (E) of the CT complexes are reported.
The solid CT complexes of the substituted-N-aryl-N-4-(-p-anisyl-
5-arylazothiazolyl)thiourea with the above acceptors have been prepared and
investigated by IR, electronic, 1H NMR and ESR spectroscopy. Nonacidic
acceptors yield complexes having π–π* and n–π* bonding. Acidic
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acceptors yield complexes having π–π* and proton transfer interaction. The
formation of 1:2 (D: A) complexes is also ascertained [138].
The reactions of the electron donor 1- methylpiperidine (1MP) with
the π- acceptors 7,7,8,8-tetracyanoquinodimethane (TCNQ),
tetracyanoethylene (TCNE), 2,3-dichloro-5,6-dicyano-p-benzoquinone
(DDQ), 2,3,5,6-tetrachloro-1,4-benzoquinone (chloranil = CHL) and iodine
(I2) were studied spectrophotometrically in chloroform at room temperature.
The electronic and infrared spectra of the formed molecular charge-transfer
(CT) complexes were recorded. The obtained results showed that the
stoichiometries of the reactions are not fixed and depend on the nature of the
acceptor. Based on the obtained data, the formed charge-transfer complexes
were formulated as [(1MP) (TCNE)2], [(1MP)(DDQ)].H2O, [(1MP)(CHL)]
and [(1MP) I] I3, while in the case of 1MP-TCNQ reaction, a short lived CT-
complex is formed followed by rapid N-substitution by TCNQ forming the
final reaction products 7,7,8-tricyano-8-piperidinylquinodimethane
(TCPQDM). The five solids products were isolated and have been
characterized by electronic spectra, infrared spectra, elemental analysis and
thermal analysis [139].
Electron donor–acceptor molecular complexes of a few phenolic
donors with some quinonoid and tetracyanoethylene acceptors have been
prepared by two different methods, i.e., by simple grinding of the respective
component pair in the solid-state and in solution. Both the methods yielded
identical dark colored 1:1 stoichiometric complexes. Spectral studies
revealed that the complexes are ionic in nature. The g values obtained in
ESR spectral studies for all these molecular adducts vary between 2.000 and
2.022, confirming the free radical nature of the adducts. The electronic
absorption spectral studies proved that the donor–acceptor complexes
formed initially, exhibit new electronic transitions at longer wavelengths, are
less stable and disassociate readily into ionic type of adducts. The absorption
maximum at longer wavelengths, i.e. ≥550 nm, are assigned to the charge
85
transfer complexes, while the new transition at around 410 ± 5 nm is
attributed to the anion radical of the adducts [140].
The kinetics and mechanism of the interaction between 2,3-dichloro-
5,6-dicyano-1,4-benzoquinone (DDQ) and ketoconazole and povidone drugs
has been investigated spectroscopically. In the presence of large excess of
donor, the 1:1 CT complex is transformed into a final product, which has
been isolated and characterized by FT-IR and GC–MS techniques. The rate
of formation of product has been measured as a function of time in different
solvents at three temperatures. The thermodynamic parameters, viz.
activation energy, enthalpy, entropy and free energy of activation were
computed from temperature dependence of rate constants. Based on the
spectro-kinetic results a plausible mechanism for the formation of the
complex and its transformation into final product is presented and discussed
[141].
Three simple, rapid and sensitive spectrophotometric procedures
were developed for the analysis of cephapirin sodium (1), cefazoline sodium
(2), cephalexin monohydrate (3), cefadroxil monohydrate (4), cefotaxime
sodium (5), cefoperazone sodium (6) and ceftazidime pentahydrate (7) in
pure form as well as in their pharmaceutical formulations. The methods are
based on the reaction of these drugs as n-electron donors with the σ-acceptor
iodine, and the π-acceptors: 2,3-dichloro-5,6-dicyano-p-benzo-quinone
(DDQ) and 7,7,8,8-tetracyanoquinodimethane (TCNQ). Depending on the
solvent polarity, different coloured charge-transfer complexes and radicals
were developed. Different variables and parameters affecting the reactions
were studied and optimized. The obtained charge-transfer complexes were
measured at 364 nm for iodine (in 1,2-dichloroethane), 460 nm for DDQ (in
methanol) and 843 nm for TCNQ (in acetonitrile). Ultraviolet–visible,
infrared and 1H-nuclear magnetic resonance techniques were used to study
the formed complexes. Due to the rapid development of colours at ambient
temperature, the obtained results were used on thin-layer chromatograms
86
for the detection of the investigated drugs. Beer's plots were obeyed in a
general concentration range of 6–50, 40–300 and 4–24 μg ml−1 with iodine,
DDQ and TCNQ, respectively, with correlation coefficients not less than
0.9989. The proposed procedures could be applied successfully to the
determination of the investigated drugs in vials, capsules, tablets and
suspensions with good recovery; percent ranged from 96.47 (±1.14) to 98.72
(±1.02) in the iodine method, 96.35 (±1.62) to 98.51 (±1.30) in the DDQ
method, and 95.98 (±0.78) to 98.40 (±0.87) in the TCNQ method. The
association constants and standard free energy changes using Benesi–
Hildebrand plots were studied. The binding of cephalosporins to proteins in
relation to their molar absorptivities was studied [142].
The charge transfer (CT) interactions between poly(N-
vinylcarbazole) (PVK) the various electron acceptors such as tetrachloro-o-
benzoquinone (o-chloranil), tetrachloro-p-benzoquinone (p-chloranil),
tetrabromo-o-benzoquinone (o-bromanil), tetracyanoethylene (TCNE),
2,3-dichloro-5,6-dicyano-p-benzoquinone (DDQ), 2,4,7-trinitrofluoranone
(TNF), I2 and Br2 have been investigated by X-ray photoelectron
spectroscopy (XPS). The interactions involving halobenzoquinones, DDQ,
I2 and Br2 resulted in the partial localization of negative charges on the
halogen sites; for that involving TCNE, the negative charges were found to
be partially localized on the cyano group. The CT interaction involving Br2
progressed beyond the mere formation of molecular complex [143].
N,N′-Bis(ferrocenylmethylidene)-p-phenylenediamine 1 and N-
(ferrocenylmethylidene) aniline 2 are readily synthesized by Schiff base
condensation of appropriate units. Iodine (I2), 2,3-dichloro-5,6-dicyano-1,4-
benzoquinone (DDQ), tetrachloro-1,4-benzoquinone (CA),
tetracyanoethylene (TCNE) and 7,7,8,8-tetracyanoquinodimethane (TCNQ)
form charge transfer complexes with 1 and 2. IR spectroscopy suggests an
increase in the amount of charge transferred from the ferrocenyl ring to the
oxidant in the order, I2<CA<TCNQ<TCNE≈DDQ. EPR spectra of the
87
oxidized binuclear complexes are indicative of localized species containing
iron- and carbon-centered radicals. The larger Fe(II)/Fe(III) ratio at lower
temperatures is best explained by a retro charge transfer from the iodide to
the iron(III) metal center. There is negligible solvent effect on the formation
of the iodine oxidized charge transfer complex of 1[144].
The formation of charge transfer (CT) complexes of
4-acetamidophenol (commonly called ‘paracetamol’) and a series of
quinones (including Vitamin K3) has been studied spectrophotometrically in
ethanol medium. The vertical ionisation potential of paracetamol and the
degrees of charge transfer of the complexes in their ground state has been
estimated from the trends in the charge transfer bands. The oscillator and
transition dipole strengths of the complexes have been determined from the
CT absorption spectra at 298 K. The complexes have been found by Job’s
method of continuous variation to have the uncommon 2:1 (paracetamol:
quinone) stoichiometry in each case. The enthalpies and entropies of
formation of the complexes have been obtained by determining their
formation constants at five different temperatures [145].
One study was interested to develop a simple, rapid and accurate
spectrophotometric method for determination of sodium flucloxacillin (fluc)
in pure form and pharmaceutical formulations. The charge-transfer (CT)
interactions between sodium flucloxacillin as electron donor and chloranilic
acid (CLA), dichloroquinone 4-chloroimide (DCQ), 2,3-dichloro-5,6-
dicyano-p-benzoquinone (DDQ) and 7,7,8,8 tetracyano-p-quinodimethane
(TCNQ), as π-electron acceptors have been investigated
spectrophotometrically. Different variables affecting the reaction were
studied and optimized. Under the optimum conditions, linear relationships
with good correlation coefficients (0.9979–0.9995) were found between the
absorbance and the concentration of the drug in the range 16–880 μg ml−1.
The proposed methods were applied successfully to the determination of the
examined drug either in pure or pharmaceutical dosage forms with good
88
accuracy and precision. The formation of the CT-complexes and the sites of
interaction were confirmed by elemental analysis CHN, UV–vis, IR, 1H
NMR and mass spectra techniques. Based on Job's method of continuous
variation plots, the obtained results indicate the formation of 1:1 charge-
transfer complexes with the general formula [(fluc)(acceptor)]. Statistical
analysis of the obtained results showed no significant difference between the
proposed method and official method [146].
Interactions of some pyrimidine derivatives, 4-amino-2,6-
dimethylpyrimidine, kyanmethin, (4AP), 2-amino-4,6-dimethylpyrimidine
(2AP), 2-aminopyrimidine (AP), 2-amino-4-methylpyrimidine (AMP), 2-
amino-4-methoxy-6-methylpyrimidine (AMMP), and 4-amino-5-chloro-2,6-
dimethylpyrimidine (ACDP) as electron donors, with iodine (I2), as a typical
σ-electron acceptor, have been studied. Electronic absorption spectra of these
interactions in several organic solvents of different polarities have performed
instant appearance of clear charge transfer (CT) bands. Formation constants
(KCT), molar absorption coefficients ( CT) and thermodynamic properties,
ΔH, ΔS, and ΔG, of these interactions have been determined and discussed
[147].
1.2.5 Inclusion Compound
The history of inclusion compounds dates back to the early nineteenth
century, with Humphrey Davy's discovery of chlorine hydrate, but the field
of inclusion phenomena, or host-guest chemistry, a subfield of
supramolecular chemistry, is growing dramatically, particularly in the last 10
years. This can be seen at a glance in Figure 1 which shows the number of
abstracts appearing in Chemical Abstracts under the term “clathrate” and
“inclusion compound” (Figure 1a) and “supramolecular chemistry”
(Figure 1b).
89
Figure 1 (a) Number of abstracts found for the terms “clathrate” and “inclusion
compound,” for the years 1950-2000. (b) Number of abstracts found for
the term “supramolecular,” for the years 1950-2000.
Inclusion Compound (inclusion complex)

A complex in which one component (the host) forms a cavity or, in
the case of a crystal, a crystal lattice containing spaces in the shape of long
tunnels or channels in which molecular entities of a second chemical species
(the guest) are located. There is no covalent bonding between guest and host,
the attraction being generally due to van der Waals forces. If the spaces in
the host lattice are enclosed on all sides so that the guest species is ‘trapped’
as in a cage, such compounds are known as clathrates or ‘cage’ compounds’.
Guest-Host Systems (Inclusion Compounds)
Inclusion compounds are typical representatives of guest-host
systems and serve as models in the field of molecular recognition. They
consist of an almost rigid host lattice with channel- or cage-like cavities
which are able to incorporate various guest molecules of quite different
chemical structure (cycloalkanes, linear alkanes, polymers). Our present
activities are focussed on the characterization of the guest components in
these systems. At present, various types of inclusion compounds (host
components: urea, thiourea, cyclophosphazenes, cyclodextrins and tri-o-
thymotide) are examined in which guests, such as substituted cyclohexanes,
six-membered ring systems and n-alkanes, are incorporated. The various
90
complexes are characterized by differential calorimetry in order to determine
the actual phase behaviour. Afterwards, dynamic solid state NMR
spectroscopy is used to provide quantitative data about the molecular order
(absolute orientation of the guests, orientational disorder, conformational
order) and dynamics (conformational, reorientational and lateral motions) of
the guest species over a large temperature range that might reach from 5 K to
380 K. So far, primarily 2H NMR investigations are performed on inclusion
compounds with selectively deuterated guest compounds. The molecular
parameters can be obtained from the analysis of variable temperature
lineshape studies, relaxation and 2D exchange experiments employing
suitable simulation programs. From this, there is access to molecular motions
that can cover several orders of magnitude. In addition, 13C MAS NMR and
FT IR spectroscopy is used for the evaluation of the conformational
properties of these systems. It is found that both the molecular dynamics and
the molecular order are strongly affected by the surrounding host matrix. In
particular, this can be seen by the changes of the guest properties in the
vicinity of solid-solid phase transitions which usually are accompanied by a
distortion of the host lattice. The above investigations also provide
information about non-bonded interactions between the various species in
such guest-host systems [148].
Cyclodextrin Inclusion Compounds
Inclusion complexes are formed between cyclodextrins and
ferrocene. When a solution of both compounds in a 2:1 ratio in water is
boiled for 2 days and then allowed to rest for 10 hours at room temperature
orange-yellow crystals form. X-ray diffraction analysis of these crystals
reveals a 4:5 inclusion complex with 4 molecules of ferrocene included in
the cavity of 4 cyclodextrine molecules and with the fifth ferrocene molecule
sandwiched between two stacks of ferrocene - cyclodextrine dimers.
Cyclodextrin also forms inclusion compounds with fragrance
molecules. As a result the fragrance molecules have a reduced vapor
91
pressure and are more stable towards exposure to light and air. When
incorporated into textiles the fragrance lasts much longer due to the slow-
release action [149].
Studies on the Inclusion Compounds of Iodine
Molecular iodine gets polarized in the electric field of the permanent
dipole lying on the host molecules. The intermolecular and the
intramolecular distances along a chain of iodine molecules gets nearly
equalized and an individual molecule becomes indistinguishable with the
formation of a long polyiodine chain. There are several inert matrices which
stabilize polyiodine chain, e.g. amylase cyclodextrins, benzamide, etc. In the
actual systems the chains of polyiodide ions are found instead of resonating
polyiodine chain.
Amylose is chemically homogeneous and a helical structure. It
forms a blue complex with iodine and hence is responsible for the blue color
of the well – known starch – iodine complex.
A birefringence of flow was observed in the starch iodine solution
revealing an anisotropic character. The iodine band at 5390 A is found to
shift towards the red part of the optical spectrum up to 6200 A or more on
this complex. The blue color of
The equilibrium for complex formation by pure PVA at room
temperature with low iodine concentration yields the values–150 kJ mol-1
and – 498 J mol-1 K-1 for the enthalpy and entropy of reaction; for a large
excess of iodine the reaction is complete. Variations in the wavelength of
maximum absorbance of the complexes correlate approximately with their
stability. Complex formation occurs through the alcohol groups of the partly
hydrolysed poly (vinyl acetate) polymers and also the residual acetate groups
of these polymers at the higher iodine concentrations [150].
The spectrophotometric and thermodynamic properties of charge—
transfer complexes of iodine and aromatic hydrocarbons have been
reinvestigated in heptane solvent to make a correlation between the
92
oscillator strength of charge - transfer bands and the heats of formation of
the complexes [151].
1.2.6 Inclusion Compounds of Iodine
The maximum absorbance of the complex is proportional to initial
polymer concentration over the range 0–100 mg dm-3 for PVA polymers
with degrees of hydrolysis in the range 75–100 mole-%, in the presence of
an excess of boric acid, iodine and potassium iodide. Within these limits 1-
mg dm-3 solutions of several commercial and laboratory-prepared polymers
have maximum absorbance 0.035 within ± ca. 3% in 1-cm cells. Sources of
error in the determination of PVA are discussed, and the reduction in the
absorbance at low iodine concentration is examined with respect to the mole-
% hydrolysis. Absorbance measurements on two solutions with,
respectively, high and low reagent concentrations allow the determination of
both the concentration of polymer and its % hydrolysis [152].
An attempt has been made to calculate the thermodynamic as well
as spectrophotometric properties of these complexes free from the influence
of iodine—solvent interaction and the results thus obtained show a good
correlation between the oscillator strength of charge—transfer bands and the
heats of formation of the complexes [153].
1.2.7. Electrical, Magnetic and Optical Properties of Biomolecular
Complexes
The electrical and magnetic properties of misfit layered cobaltocene
complexes of composition (PbS)1.18 (TiS2)2(CoCp2)0.28,
(PbS)1.14(TaS2)2(CoCp2)0.28, and (PbSe)1.12(NbSe2)2(CoCp2)0.27 [Cp = C5H5-]
were investigated. All the pristine chalcogenides studied exhibit a metallic
behavior and a magnetic susceptibility virtually independent of temperature.
Moreover, the Ta and Nb compounds the later impurified with NbSe2
undergo a superconducting transition at low temperatures (TC < 4 K). Upon
cobaltocene intercalation, the Ta and Nb systems behave similarly. The
superconducting transition temperature changes very little and the
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metallic behavior is preserved: the susceptibility is temperature-
independent, whereas the resistivity increases with increasing temperature.
This is consistent with an electron transfer from the metallocene to the host.
The Ti intercalate behaves markedly differently [154].
Charge-transfer complexes formed by reaction of 2,3,7,8-
tetramethoxychalcogenanthrenes(5,10-dichalcogenacyclo-diveratrylenes,
‘Vn2E2’) with 7,7,8,8-tetracyanoquinodimethane (TCNQ) are prepared and
their structures are determined. Spin concentration, mobilities and gap
energies of the polycrystalline samples are evaluated from e.s.r. intensities
and electrical conductivity measurements. The influence of the different
chalcogen atoms on physical properties is discussed [155].
Recently one has studied a charge transfer interaction between
TCNQ and several surfactants in aqueous solutions (1). In this article we will
report an interaction between cationic surfactant such as dodecylpyridinium
chloride and 2, 5-dichloroquinone from the point of a view of charge transfer
interaction and will compare the results with the results of interaction of
TCNQ [156].
The formation of charge-transfer (CT) complex to increase the
conductivity has been the subject of intense research activity for the past
decades. Those CT complexes have been used as organic semiconductors in
field effect transistors (FETs), charge injection and transport materials in
organic light-emitting diodes (OLEDs) and organic photovoltaic (OPV)
cells. A serial was of new CT complexes with polymers as donor and TCNQ
as acceptor were prepared. The polymers are polycarbazoles with various
content of carbazole moiety in the back chain. The X-ray crystal structure of
the model compound 4,4′-bis (N-carbazolyl)-1,1′-biphenyl(CBP)/TCNQ
complex showed the formation of 2:1 stack structure (with 1:1 carbazole
moiety: TCNQ ratio). The polycarbazole/TCNQ complexes form uniform
films by spin-coating. Devices with the structure of ITO/polycarbazole:
TCNQ complex/Mg: Ag were fabricated. The current–voltage
94
characteristics showed that the devices exhibit much higher conductivity
compared to their analogy ITO/polycarbazole/Mg: Ag structure devices
[157].
Two simple, rapid and sensitive spectrophotometric methods have
been proposed for the determination of lisinopril in pure form and
pharmaceutical formulations. The methods are based on the charge transfer
complexation reaction of the drug with 7,7,8,8,tetracyanoquinodimethane
(TCNQ) and p-chloranilic acid (pCA) in polar media. The lisinopril–TCNQ
and lisinopril–pCA charge transfer complexes dissociate in acetone and
methanol, respectively, and yield coloured TCNQ and pCA radical anions
which are measured spectrophotometrically at 743 and 525 nm. Under
optimised experimental conditions, Beer's law is obeyed in the concentration
range of 2–26 and 25–300 μg ml–1 with molar absorptivity of 1.432 × 104
and 1.192 × 104 l mol–1 cm–1 for TCNQ and pCA methods, respectively.
Both the methods have been applied to the determination of lisinopril in
pharmaceutical dosage forms. Results of analysis are validated statistically
[158].
The synthesis and the redox behaviour of electroactive donor
molecules incorporating an azino spacer group between a benzoselenazole
core and another heterocyclic moiety, either a benzoselenazole one or a
thiazole one, are reported. Neutral complexes were obtained with TCNQ
and, for the first time with dithiadiazafulvalene or diselenadiazafulvalene
derivatives, cation radical salts by electrocrystallization. Crystal structures
data of these complexes are presented and their geometries compared with
those deduced from theoretical calculations [159].
The possibility of opening cyclic iminoethers and forming linear
polymers or copolymers under the action of charge transfer complexes has
been studied. The polymerization of 2-methyl-2-oxazoline, acting as donor,
proceeds in the presence of various organic electron-acceptors such as
tetracyanoethylene 7,7,8,8-tetracyanoquinodimethane and
95
2,4,7-trinitrofluorenone. Initiation takes place by charge transfer complexes
formed between the monomer and the acceptor. With acceptors which
possess polymerizable bonds, i.e. tetracyanoethylene and
tetracyanoquinodimethane, copolymers are obtained [160].
The particular study was interested to develop a simple, rapid and
accurate spectrophotometric method for determination of sodium
flucloxacillin (fluc) in pure form and pharmaceutical formulations. The
charge-transfer (CT) interactions between sodium flucloxacillin as electron
donor and chloranilic acid (CLA), dichloroquinone 4-chloroimide (DCQ),
2,3-dichloro-5,6-dicyano-p-benzoquinone (DDQ) and 7,7,8,8 tetracyano-p-
quinodimethane (TCNQ), as π-electron acceptors have been investigated
spectrophotometrically. Different variables affecting the reaction were
studied and optimized. Under the optimum conditions, linear relationships
with good correlation coefficients (0.9979–0.9995) were found between the
absorbance and the concentration of the drug in the range 16–880 μg ml−1.
The proposed methods were applied successfully to the determination of the
examined drug either in pure or pharmaceutical dosage forms with good
accuracy and precision. The formation of the CT-complexes and the sites of
interaction were confirmed by elemental analysis CHN, UV–vis, IR, 1H
NMR and mass spectra techniques. Based on Job's method of continuous
variation plots, the obtained results indicate the formation of 1:1 charge-
transfer complexes with the general formula [(fluc)(acceptor)]. Statistical
analysis of the obtained results showed no significant difference between the
proposed method and official method [161].
Charge transfer complexes of tetracyanoquinodimethane (TCNQ)
(namely TTT-TCNQ and TTT-TCNQ2), are prepared with the radical cation
of tetrathiotetracene (TTT). The two salts are conductive at room
temperature and show (at low temperatures) a quasi constant paramagnetism
and a linear specific heat term. This behaviour which is characteristic of a
96
magnetic ground state as already found in other salts with regular TCNQ
stacks is discussed [162].
Study of the synthesis of four asymmetric partially selenated
tetrathiafulvalenes (TTFs), EDS-TTF Ia (ethylenediselena-TTF), EDS-
DMTTFIb (EDS-dimethyl-TTF),EDS-DCMTTFIIa (EDS-dicarbomethoxy-
TTF) and EDS-DHMTTF IIb (EDS-dihydroxymethyl-TTF), using different
routes is depicted. The preparation of both a charge transfer complex, Ib-
TCNQ (Ib-tetracyanoquinodimethane), and a new radical cation salt, IIb-
ClO4, is presented [163].
The crystal structure for the charge transfer complex of the title
hydrogen-bonded (H-bonded) charge-transfer (CT) complex indicates and
alternated stacking of the naphthalene moiety and chloranil, which contain
no direct H-bonding between the donor and the acceptor. The complex
showed only a little change in stretching frequencies to the applied pressure.
Therefore, as a design strategy for new interesting materials, it seems
important to obtain CT complexes with direct H-bonding between the donor
and acceptor [164].
The 3,6-dicyano-1,2,4,5-tetrazine and the 2,4,6-tricyano- -triazine
are found good electron acceptors for forming charge transfer complexes; the
former gave with tetrathiofulvalene a 1:1 charge transfer complex of good
electric conductivity, thus proving that the attainment of aromaticity in the
radical anion is not a necessary requisite for conductivity [165].
The new charge transfer complex t-TTF-TCNQ, whose unsymmetric
cation is intermediate between TTF and HMTTF, presents a regular stacking
of both donor and acceptor chains. We show that this compound has a
metallic behavior at high temperatures and undergoes one metal-insulator
transition near 81 K. Its electrical and magnetic properties are examined in
connection to this phase transition and the effective dimensionality [166].
The electrical and magnetic properties of misfit layered cobaltocene
complexes of composition (PbS)1.18(TiS2)2(CoCp2)0.28,
97
(PbS)1.14(TaS2)2(CoCp2)0.28, and (PbSe)1.12(NbSe2)2(CoCp2)0.27 [Cp = C5H5-]
were investigated.The complex undergoes a metal semiconducting transition
below 70 K, and the magnetic data are significantly temperature-dependent
[167].
The charge transfer interaction between hexylamine (HA) and
7,7,8,8-tetracyanoquinodimethane (TCNQ) and the fluorescence behaviour
of the charge transfer complex were studied in non-aqueous solvents
(dichloromethane, chloroform, carbon tetrachloride, heptane, iso-octane,
decane and cyclohexane) and in sodium bis(2-ethyl-hexyl)sulphosuccinate
(AOT)-cyclohexane reverse micellar medium and water-AOT-cyclohexane
microemulsion medium. A 1:1 charge transfer complex between HA and
TCNQ was formed, and its binding strength was estimated by the Benesi-
Hildebrand equation. The charge transfer complex was fluorescent; this was
hindered by AOT and by a higher concentration of HA. The results were
analysed using the Stern-Volmer equation [168].
Charge transfer (CT) complexes of tetrathiafulvalene bisannulated
24-crown-8 (1) with tetrafluoro (F4)-, 2,5-dibromo (Br2), 2,5-dichloro (Cl2)-
tetracyanoquinodimethane (TCNQ), and 2,3-dicyano-5,6-dichloro-p-
benzoquinone (DDQ) were prepared. The electronic ground state of the
acceptor varies from the completely ionic to partial charge transfer state.
Within the CT complexes the donor 1 was completely oxidized to the
divalent cationic state 12+. The molecular conformation of 12+ in Cl2-TCNQ
complex was an intra-dimer form folded over the flexible part of
macrocyclic 24-crown-8 [169].
A new charge-transfer compound PANT-TCNQ (PANT=9-
phenylanthracene, TCNQ=7,7,8,8-tetracyanoquinodimethane) has been
prepared from 7,7,8,8-tetracyanoquinodimethane (TCNQ) and 9-
Phenylanthracene in dichloromethane at room temperature. The conductivity
of the compound, at room temperature is 2.08×10−9 S cm−1. The temperature-
dependence of electrical conductivity of the PANT-TCNQ compound
98
exhibits a semiconductor behavior. The optical spectra indicate that the
compound has a direct band gap (2.46±0.15 eV) due to direct transition
[170].
The dielectric constant of the phenothiazine-iodine system in
benzene has been determined at 30°C and 40°C on a dipolemeter operating
at a radiofrequency of 1MHz. Simultaneous determination of density had
been made on a calibrated pyknometer. The dipole moment of the donor, μD
(calc.), has been compared with the dipole moment μN of 1:1 molecular
complex formed between donor-acceptor at two temperatures. The μN values
at 30°C & 40°C are for chloropromazine-I2 13.4 D & 12.6 D;
prochloroperazine -I2, 13.5 D & 11.6 D; promazine-I2, 21.2 D & 17.3 D;
pericyazine -I2, 12.9 D & 10.5 D and thioproperazine -I2, 19.6 D & 12.0 D;.
High values of E HOMO for the donor molecule suggest that the
phenothiazines are good donors and the possibility of molecular association
with σ-acceptor iodine is from the active site at S atom in each donor. The
extent of molecular association decreases with the increase in temperature
[171].
1,5-Dimethoxynaphthalene (1,5-DMN) and 2,3-DMN were
synthesized using the phase transfer catalysis (PTC) technique. Their
fluorescence is quenched by 7,7,8,8 -tetracyanoquinonedimethane (TCNQ)m
picric acid, chloranil and bromanil. The quenching rate constant values kq
were estimated. It was found that the rate of quenching of 2,3-DMN is
slower than that of 1,5-DMN by the same acceptors. The role of the solvent
polarity on the efficiency of fluorescence quenching og 1, 5-DMN with
picric acid was also studied. Spectral studies show that 2,3-DMN forms 1:1
charge transfer complexes (CTCs) with different π-acceptors in
dichloromethane, while 1,5-DMN forms contact CTCs with TCNQ,
chloranil and bromanil and 1:1 CTCs with tetracyanoethylee (TCNE) and
picric acid. The equilibrium constants and thermodynamic standard reaction
quantities of the CTCs were estimated [172].
99
Infrared spectra of the charge transfer complexes between nine
organic sulfides (as well as diethylselenide) with iodine were recorded
between 1500 and 400 cm−1 in CS2 and CCl4 solutions and in the region 600-
50 cm−1 in C6H12 and C6H6 solutions. Raman spectra of the complexes were
recorded below 600 cm−1. For each system, i.r. and Raman bands in the 200-
160 cm−1 were assigned to the I---I stretching mode of the complex.
Additional i.r. bands below 160 cm−1, absent in Raman, were ascribed to
intermolecular S---I stretching vibrations. The integral intensities of these
bands were determined and correlated with the thermodynamic functions.
Some Raman active fundamentals of 1,4-dithiane became i.r. active in the
iodine complex in accordance with a break down of the C2h symmetry. A
force constant calculation was carried out for the dimethylsulfide-iodine
complex and simplified calculations of the three point mass models were
made for all the systems [173].
Optical characterization of the charge transfer complex of
2,9,16,23-tetra neopentoxyphthalocyaninatozinc(II) with 2,3-dichloro-5,6-
dicyano-p-benzoquinone (DDQ) has been carried out using the transmittance
T(λ) and reflectance R(λ) spectra. The optical band gap and Urbach energies
were calculated from the optical absorption spectra. The optical absorption
spectra show that the absorption mechanism is a direct transition. The optical
constants (refractive index n, extinction coefficient k, dielectric constants
ε1, ε2) of the compound were determined. Optical dispersion parameters
Eo and Ed developed by Wemple–DiDmenico were calculated [174].
Formation of molecular charge transfer (CT) complexes of some
polyenes with iodine has been confirmed by spectroscopic studies. The dark
and photoconductive properties of these CT complexes have been
investigated in a sandwich cell. Both the dark and photoconductivity
increases by several orders of magnitude by complex formation. The
measured thermal activation energy is identical for dark and
photoconduction in the complexes. Similar photoconduction action
100
spectra in pure and in iodine-complexed polyenes suggest the same
photocarrier generation mechanism to be operative in both the cases.
Spontaneous generation of carriers by CT interaction and their migration by
trapping and detrapping mechanisms seems to be responsible for electrical
conduction in the CT complexes [175].
It is to be described that how single-molecule sensitive
fluorescence resonance energy transfer (FRET) and photoinduced electron
transfer (PET) reactions can be successfully applied to monitor
conformational dynamics in biopolymers. Single-pair FRET experiments are
ideally suited to study conformational dynamics occurring on the nanometer
scale, e.g. during protein folding or unfolding. In contrast, conformational
dynamics with functional significance, for example occurring in enzymes at
work, often appear on much smaller spatial scales of up to several
Angströms. Our results demonstrate that selective PET-reactions between
fluorophores and amino acids or DNA nucleotides represent a versatile tool
to measure small-scale conformational dynamics in biopolymers on a wide
range of time scales, extending from nanoseconds to seconds, at the single-
molecule level [176].
The charge-transfer (CT) reaction between 7,7,8,8-
tetracyanoquinodimethane (TCNQ) as a π-electron acceptor and cinnarizine,
analgin, norfloxacin as electron donors have been studied by
spectrophotometric method. The charge transfer complexes between TCNQ
and these drugs have stable blue color, therefore a simple, rapid, accurate
and sensitive method for determination of these drugs has been developed.
The optimization of the experimental conditions is described. Beer’s law is
obeyed in the ranges 2–18, 2–18 and 4–32 μg/ml for cinnarizine, analgin and
norfloxacin, respectively. The apparent molar absorptivity of CT complexes
at 743 nm is 1.58×104, 1.71×104 and 8.91×103 l/mol per·cm, respectively.
The composition of all these CT complexes are found to be 1:1 by different
methods. The relative SDs are less than 3% (n=10). The proposed
101
method has been applied to the determination of these drugs in their each
pharmaceutical dosage forms with satisfactory results [177].
The magnetic properties of the charge transfer salts Qn(TCNQ)2,
Cs2(TCNQ)3 and TTF—TCNQ in the form of single crystals and after strong
pressing or grinding to a fine powder, which introduces lattice defects and
increases the surface area. It is found that for the former two compounds
pressing or grinding leads to a non-linear, saturating component in the
magnetisation field curves, whereas the effect is absent for TTF—TCNQ. It
is suggested that this behaviour could arise from strongly coupled localised
spins at the surface, i.e. surface magnetism in these materials [178].
A series of the charge-transfer compounds determined as 1:1
stochiometric ratio by Job method has been prepared with the interaction of
7,7,8,8-tetracyanoquinodimethane (TCNQ) and anthracene, 9-
methylanthracene, 9-bromanthracene in dichloromethane at room
temperature. The values of the optical band gap Eg, and Urbach energy E0
were determined from the optical absorption. The optical absorption
measurements indicate that the absorption mechanism is due to allowed
direct transitions for the compounds and it is evaluated that the optical band
gap and Urbach energy values changes with incorporating R group in the
compounds. The optical constants such as refractive index n, and extinction
coefficient k and real and imaginary part of dielectric constant and optical
conductivity of the compounds were calculated. Eg and E0 reflect the
influence of different types of disorder on the absorption spectra processes.
Thus, a correlation between Eg and E0 was made. Form this correlation, G
value that is proportional to the second-order deformation potential and, Ef
value that depend on local coordination, parameters are found to be 0.29 and
2.37 eV, respectively [179].
In the charge-transfer (CT) solubilization of 7,7,8,8-
tetracyanoquinodimethane (TCNQ) by homogeneous nonionic surfactants,
the amount of solubilized TCNQ and the cloud point and electric
102
conductivity of the CT complex solution were investigated. The amount of
solubilized TCNQ was spectrophotometrically determined by using the color
development due to the CT interaction between TCNQ and the nonionic
surfactant micelle. The cloud point and electric conductivity of the micelle
solutions solubilizing TCNQ increased with increasing TCNQ concentration.
These phenomena were explained in terms of partial ionization in the
hydrophilic portion of nonionic surfactants attributed to the charge transfer
from oxygen atoms in polyethyleneoxide chains to TCNQ [180].
Preparation of conductive polycarbonate and polystyrene films
using tetrathiotetracene (TTT) and TCNQ with different input molar ratio of
TTT: TCNQ even as high as 7:1 i.e. with big excess of the donor (TTT) is
reported. Conductive systems (conductivity of the order of 10−3 − 10−4 S/cm)
containing only 0.037wt.% of TCNQ are obtained. Conducting polymers
with so low content of TCNQ have never been obtained before. The total
additive content (TTT+TCNQ) in these system is also very low (in some
cases less than 0.4wt. %) and the content of 1:1 CT complex is of the order
of 0.1wt. %. Scanning electron microscope pictures show that the conductive
network in these systems consist of very thin (ca.50nm in diameter)
whisker-like crystallites of the additive [181].
The formal of 1:1 charge transfer complex (BTV-TCNQ) have been
studied by the UV-Vis, FT-IR, XPS and ESR spectroscopies. The results
show that partial charge transfers occur between π-donor and π-acceptor, the
room temperature conductivity is 33Scm−1, however, the temperature-
dependence conductivity indicates that the CT complex shows
semiconductor behavior, the activation energy for conduction is 0.06eV
[182].
Copper (II) and nickel (II) biguanides and O-alkyl-1-amidinourea
can act as donors for the formation of charge transfer (CT) adducts with I2
and tetracyanoquinodimethane (TCNQ) as acceptors. Iodine adducts are
characterized both in solid and solution states whereas TCNQ adducts
103
obtain only in solution. Appearance of a broad band at 355 nm for iodine
adducts and at 335 nm for TCNQ adducts and shifting of i.r. frequencies
support the formation of donor acceptor associates. Elemental analysis
establishes 1:1 stoichiometry of the solid adducts. The K and values
determined by modified Benesi—Hildebrand, Scott and Rose—Drago
equations are found to be of the order of 104 and 103 respectively at 298 K in
methanol [183].
Glucose oxidase entrapped in the layer near the electrode surface of
conductive charge-transfer complexes or on glassy carbon electrodes
modified by tetracyano-quinodimethane (or by its K-salt) catalyzes the
electrochemical oxidation of glucose in the interval from −0.05 to 0.4 V
(vs. AgAgCl). When enzyme electrodes operate in a switched-off state the
charge is accumulated in the complexes. The components of the complexes
oxidize the active center of glucose oxidase. A scheme for electrocatalytic
oxidation of glucose by mediators is proposed [184].
Electrical conductivity and spectral properties (UV-VIS absorption
and especially the temperature dependence of IR absorption) are studied for
the simple salt 1-methyl-3-propyl-imidazolium 7,7,8,8-tetracyano-p-
quinodimethane (MPI+ TCNQ−√. The temperature dependence of the IR
absorption coefficient for the bands due to activation of the mode Ag is
discussed in terms of changes in energy level population, geometry, and
electron interactions. The temperature dependence of the absolute number of
the TCNQ dimers in the triplet state is measured independently using the
EPR method. The temperature dependences of the ground (singlet) state
population of the TCNQ dimers and of the singlet—triplet energy separation
J(T) = [(0.18 ± 0.01)-(2.5 ± 0.5) × 10−4 T] eV were determined from this
measurement. These values lead to an unrealistically large value of the linear
temperature expansion coefficient within the framework of the simple
isolated model of dimers. Therefore, the weakly interacting model of dimers
should be preferred [185].
104
The interaction between ketoconazole and povidone drugs with
iodine was found to proceed through initial formation of a charge transfer
(CT) complex as an intermediate. The stoichiometry of the complex was
found to be 1:1 in the case of povidone–iodine system and 1:2 in the case of
ketoconazole–iodine system and the same was confirmed by thermal
(TGA/DSC) studies. The formation of I3− species was confirmed by
electronic and laser Raman spectra. The three peaks appeared in Raman
spectra, of the isolated adducts corresponds to νas(I–I), νs(I–I) and δ(I3−),
confirmed the presence of asymmetric I3− ion. The rate of the interaction has
been measured as a function of time and solvent. The pseudo-first-order rate
constants at various temperatures for the interactions were measured and the
activation parameters (ΔG#, ΔS# and ΔH#) were computed. Based on the
spectral and spectrokinetic evidences a mechanism involving the formation
of a polar intermediate and its conversion to the final product has been
proposed and discussed [186].
The influence of complexing agents such as methanol, ethanol, 1-
propanol, 1-butanol, 1-pentanol, 1-hexanol, cyclohexanol and 2-octanol on
the formation of a blue coloured amylose · iodine complex (pH 4.8), under
suboptimum concentrations of iodine and in the absence of potassium iodide,
is studied by recording the absorbance at 640 nm. A drop in absorbance at
640 nm accompanied by a blue shift in the spectrum (580–640 nm) was
observed at higher concentration of the complexing agents. This behaviour
of amylose partially complexed with iodine appears to be due to ligand-
induced structural changes in the amylose chain. The fall in absorbance at
640 nm observed when the temeprature of amylose · Ioidine complex in the
presence of complexing agents is raised, and the subsequent regeneration of
the absorbance on cooling, indicates the possible helix to random coil
transition of the amylose chain in an aqueous system [187].
The electron donor acceptor complexes of iodine with
phospholipids such as phosphatidylethanolamine (PE),
105
lysophosphatidylcholine (LPC) and sphingomyelin (SM) have been studied
spectrophotometrically in cyclohexane solution as well as in solid film. From
the results, the electron donating properties of phospholipids towards iodine
have been compared including the earlier results of iodine complex with
phosphatidylcholine (PC). Thus the electron donor strengths of the
phospholipids studied are in the order: SM > PC > LPC > PE. The calculated
ionization potentials of phospholipids from the charge-transfer bands are in
the range 6.72–6.79 eV [188].
1.3 Absorption of radiation by semiconductors
The fundamental absorption in a semiconductor refers to interband

(band –to – band) or to exciton transition. There is excitation of an electron
from the valence band to conduction band. There is a rapid increase in
absorption in the band gap region of frequency. There is threshold near Eg
(band gap) and this is called absorption edge.
The moment of a photon is very small compared to the momentum of
the crystal. The phonon absorption process conserves the momentum of an
electron. The absorption coefficient is proportional the probability of
transition and densities of states of initial and final states [189].
1.3.1 Allowed irect transition
In the absorption transitions between two
direct valleys all the momentum
conserving transitions are allowed. The
initial and final states are related by
Ef = h - Ei for parabolic bands as shown
in the Figure 1.
Figure 1
106
2k 2 2 k 2
(Ef – Eg) = and Ei =
2me* 2mh*
2k 2  1 1  2k 2
Therefore, h  Eg =   
2  mh * me *  2mr
The density of states is given by

8 k 2 dk (2mr )3/ 2
N (h ) d (h ) = = (h  Eg )1/ 2 d (h )
(2 )3 2 2 3
where mr is the reduced mass. This shows that (h) = A (h-Eg)1/2, A is a

constant. Thus in allowed direct transition the absorption coefficient is
proportional to (h - Eg)1/2 .
1.3.2 Forbidden direct transition
In some materials, quantum selection rules forbid direct transitions at
k=0 but allow them at k  0. The transition probability increases with k2,
which is proportional to (h - Eg). The density of states is proportional to (h
- Eg)1/2. Thus the absorption coefficient is proportional to (h - Eg)3/2 ,
B
i .e,  h = A (h - Eg)3/2 where A is given by A = , here B is a constant.
h
Thus,
 h = B (h - Eg)3/2.
1.3.3 Indirect transitions
When a transition requires a change in both energy
and momentum and since a photon can not provide momentum, a
two – step process occurs. A phonon is a quantum of lattice
vibration. A phonon of the required momentum change is used in
a two – step process as shown in the Figure 2.
If E p is the phonon energy, h e = E f - E i + E p , h a = E f - E i - E p
for emission and absorption of phonons.
107
The densities of states at E i and E f are
given by
1
N (E i ) = (2m h * ) 3 / 2 Ei 1 / 2 and
2 2 3
1
N (E f ) = (2m e * ) 3 / 2 (E f – Eg) 1 / 2
2 
2 3
Figure 2
1
Thus, N (E f ) = (2m e * ) 3 / 2 (h- E g  E p + E i ) 1 / 2
2 
2 3
By integrating above all possible combinations of states,
A (h - Eg - Ep) 2 A (h - Eg + Ep) 2

 a (h) = and  e (h) =
 Ep   Ep 
exp   1 1  exp   
 kBT   kBT 
The total  is given by  =  e +  a .

 a is valid for h  E g – E p and  e is
valid for h  E g + E p .
Thus there is break in the straight

line plot of  1 / 2 vs h. There fore
there is a change in slope as indicated
in the Figure 3.
Figure 3
1.3.4 Band tailing

There is a perturbation of the bands by the formation of
tails of states extending the bands into the forbidden energy gap.
This happens due to impurities. An ionized donor exerts
attractive and repulsive forces on electrons and holes,
respectively. The densities of states lead to conduction band
states at lower potential and valence band states at higher
108
potential. At high concentrations of impurities, the impurity
states from a band whose distribution tail in to the energy gap.
Also there is deformation potential. A local mechanical strain is generated by
impurities. Either there is compression or dilation. Compression increases
energy gap and dilation reduces energy gap. Dislocations generate similar
effect.
Because of the above – discussed band tailing effects, one finds an
exponentially increasing absorption edge rather than a sharp cut – off with
d (ln  ) 1
step function. It is found that  and this is called Urbach’s rule.
d (h ) KBT
The final states form an exponential tail described by Nf = No e E/Eo. Here Eo

1
 d (ln  ) 
is called the width of the tail and is calculated by Eo   
 d (h ) 
1.5.5 Burstein – Moss shift

If a semiconductor is heavily doped, the Fermi level is inside the band
(the conduction band in an n – type material) by a quantity n as shown in
the Figure 4.
The states below n are already filled, and
transitions to states below Eg + n are
forbidden. Thus absorption edge shift to
higher energies by about n. This shift in
the absorption due to band filling effect is
called Burstein – Moss shift. In n- type
germanium only phonon emission occurs
and edge is shifted to Eg + Ep +n.
Figure 4
109
In heavily doped indirect – gap semiconductors, momentum is conserved by
electron – electron scattering or impurity scattering. The scattering
probability is proportional to the number N of scatters and
 = AN (h- Eg - n)2 where A is constant. Heavy doping leads to an
effective shrinkage of the energy gap.
1.3.6 Free – carrier absorption
The Drude model leads to f  2 where f is the absorption by free
carrier and  is the wavelength of light. Thus in a metal f is proportional to
2.However, in a semiconductor the absorption by free carrier in a
conduction band occurs in a region h  Eg and is proportional to p where p-
can range from 1.5 – 3.5. The electron must make a transition to a higher
energy state within the same valley for absorbing a photon. The transition
requires an additional interaction for conserving momentum. The change in
momentum can be provided by interaction with phonons or ionized
impurities. The collision with the semiconductor lattice results in scattering
by acoustic phonon leading to absorption increasing as 1.5. Scattering by
optical phonons gives a dependence of 2.5while scattering by ionized
impurities gives dependence on 3 or 3.5.
In general, when all the three processes contribute and resultant
absorption coefficient is given by,
f = A 1.5 + B 2.5 + C 3.5 where A, B and C are constants.
The dominant mode of scattering will depend on the impurity concentration.
It is found by experience that f  3 for neutral impurities, f  3.5
for negatively charged impurities, f  4 for positively charged hydrogen –
like impurities and f  5 for impurity band scattering.
From a detailed account of light absorption by electrons [190] in
  EI
localized states, 
  [   2m *(  EI ]4
2 2 2 2
110
Where EI is the impurity ionization potential. The quantity -1/2 is equal to
the distance at which the probability of locating the electron decreases e
times.  increases linearly with frequency for   2 EI and passes through a
maximum then decreases at first slowly (  1 ) but much faster in the end.
For EI very less than  ,  f   5 or  f   5 from the above equation.
The theory of absorption of radiation of the hydrogen atom may be
applied to the localized states with hydrogen – like spectrum, then the
absorption coefficient is given by
  EI    EI 
4 exp  4  1    arctan 1  
2  e  EI        
10 2 2
  Nloc 
  X
3ncm * EI     EI 
1  exp  2  1 
   
where n is refractive index, EI is the impurity ionization energy and m * is the

effective mass. For EI   ,  f   4   4 for hydrogen – like impurities from
the above equation.
111
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Chapter 1

Introduction: Important Biomolecules

Amylose forms a colloidal dispersion in hot water whereas

Amino acids exist in either D (dextro) or L (levo) form

Grouped table of twenty amino acids' structures, nomenclature, and their

Asn = asparagine Asp = aspartic acid

Cys = cysteine Gln = glutamine

Glu = glutamic acid Gly = glycine

Leu = leucine * Lys = lysine *

The amino acid selenocysteine

Non-standard amino acids

3-dimensional structure of hemoglobin, a globular protein.

Three possible representations of the three-dimensional structure of the protein triose

Most proteins fold into unique 3-dimensional structures. The shape

(Red-Blood-Cell Plasma Membrane)

Chemical structure of DNA. Hydrogen bonds shown as dotted lines.

A hairpin loop from a pre-mRNA.

The common fatty acids of animal and plant origin

Systematic name Trivial name Saturated Shorthand

ethanoic acetic 2:0

butanoic butyric 4:0

hexanoic caproic 6:0

octanoic caprylic 8:0

decanoic capric 10:0

dodecanoic lauric 12:0

hexadecanoic palmitic 16:0

octadecanoic stearic 18:0

eicosanoic arachidic 20:0

docosanoic behenic 22:0

Monoenoic fatty acids

cis-9-hexadecenoic palmitoleic 16:1(n-7)

cis-6-octadecenoic petroselinic 18:1(n-12)

cis-9-octadecenoic oleic 18:1(n-9)

cis-11-octadecenoic cis-vaccenic 18:1(n-7)

cis-13-docosenoic erucic 22:1(n-9)

cis-15-tetracosenoic nervonic 24:1(n-9)

Polyunsaturated fatty acids*

9,12-octadecadienoic linoleic 18:2(n-6)

6,9,12-octadecatrienoic γ-linolenic 18:3(n-6)

9,12,15-octadecatrienoic α-linolenic 18:3(n-3)

5,8,11,14-eicosatetraenoic arachidonic 20:4(n-6)

* all the double bonds are of the cis configuration

The latter form of the nomenclature is of special value to

- and in conjugated linoleic acid (mainly, 9-cis,11-trans-octadecadienoate) or

Branched-chain fatty acids are synthesised by many microorganisms (most

Phytanic acid, 3,7,11,15-tetramethylhexadecanoic acid, is a

The structure of ATP has an ordered carbon compound as a backbone,

ATP + H2O → ADP + Pi

The energy-carrying part of an ATP molecule is the triphosphate "tail"

Functions of Steroid Hormones

Quantum mechanically, this is described as a resonance between the

The positioning of the characteristic CT bands in the electromagnetic

thermodynamic standard reaction quantities (ΔG°, ΔH° and ΔS°), oscillator

Inclusion Compound (inclusion complex)

The fundamental absorption in a semiconductor refers to interband

The density of states is given by

where mr is the reduced mass. This shows that (h) = A (h-Eg)1/2, A is a

By integrating above all possible combinations of states,

A (h - Eg - Ep) 2 A (h - Eg + Ep) 2

The total  is given by  =  e +  a .

Thus there is break in the straight

1.3.4 Band tailing