1

Acknowledgement

With all my heart, I would like to express my gratitude towards Dr.

Avinash Singh, Dr. Zameer Ahmed, Dr. Faazil Shaikh, Ms. Rukhsaar
Shaikh and Mrs. Farha Pathan for their moral support and guidance
towards the completion of the On Job Training Project.
With due respect, I would like to sincerely thank our honorable Principal,
Dr. Iqbal N. Shaikh for inspiring me and guiding me throughout my
project and giving me valuable suggestions.
I would like to thank my family and friends and all others for their
blessings, moral support and their help which I received knowingly and
unknowingly throughout my work.

Heebanaaz Sabir Sayyed

 2

INDEX

Sr. No. Content Page No.

1 Introduction 3

2 Use of lab instruments and equipment 5

3 UV-Visible and IR Spectroscopy 20

4 Gas Chromatography 29

5 IPR (Intellectual Property Rights) 37

47
6 Basic techniques

7 Pharma Industry and APIs 51

8 Drug Designing 66

9 Softwares in Chemistry 70

10 Conclusion 78
 3

Introduction
The On-the-Job Training (OJT) program in chemistry is an initiative that is designed
to provide participants with practical experience and hands-on learning opportunities
in various aspects of the chemical sciences. Whether you're a student, a recent
graduate, or an aspiring professional, OJT offers a valuable pathway to gaining real-
world insights and expertise in the field of chemistry.
Basic Techniques in Chemistry
In the realm of chemistry, mastering fundamental techniques is essential for
conducting experiments safely and effectively. Some basic techniques include:
1. Measurement and Weighing: Accurate measurement and weighing of
chemicals and reagents are crucial for precise experimental results.
2. Mixing and Stirring: Proper mixing and stirring techniques ensure
homogeneity and consistency in solutions.
3. Filtration: Filtration is used to separate solids from liquids or to remove
impurities from solutions.
4. Titration: Titration is a method used to determine the concentration of a
substance in solution by reacting it with a known reagent.
5. Distillation: Distillation is a process used to separate components of a
mixture based on differences in their boiling points.
Use of Laboratory Equipment
A wide array of laboratory equipment is utilized in chemical experiments.
Familiarity with the following equipment is essential:
1. Balances and Weighing Instruments: Used for precise measurement of mass.
2. Glassware (Beakers, Flasks, Pipettes): Essential for preparing and measuring
solutions.
 4

3. Heating Equipment (Bunsen Burners, Hot Plates): Used for heating and
conducting various reactions.
4. Spectrophotometers: Instruments used to measure the absorption or emission
of light by chemical substances.
5. Chromatography Systems: Including Gas Chromatography (GC) and High-
Performance Liquid Chromatography (HPLC), used for separating and
analyzing mixtures.
Specialized Areas in Chemistry
Chemistry encompasses a wide range of specialized fields, including:
1. UV and IR Spectroscopy: Techniques used to analyze the molecular
structure of compounds based on their absorption or emission of ultraviolet
(UV) and infrared (IR) radiation.
2. Gas Chromatography (GC): A technique used to separate and analyze
volatile compounds in a mixture.
3. Intellectual Property Rights (IPR): Understanding patent laws and
regulations is essential for protecting intellectual property rights associated
with chemical innovations.
4. Pharmaceutical Industries and Active Pharmaceutical Ingredients (API): The
pharmaceutical industry involves the development, manufacturing, and
marketing of drugs, including APIs, which are the active components
responsible for the therapeutic effects of medications.
5. Drug Designing and Software Applications: Utilizing computer-aided design
(CAD) software and molecular modeling techniques for rational drug design
and discovery.
 5

Use of Lab Instruments and Equipment

Laboratory instrumentation is the use or application of instruments for observation,
measurement, or control. It involves the use of or operation with instruments;
especially: the use of one or more instruments in carrying out laboratory tests.
The use of UV spectrophotometry (to measure light intensity) and gas
chromatography. Laboratory instrumentation is a collection of laboratory test
equipment. Such a collection of equipment might be used to automate testing
procedure. It could also include: "The design, construction, and provision of
instruments for measurement, control, etc. the state of being equipped with or
controlled by such instruments collectively."
Bunsen burners, flasks, microscopes, burettes, pipettes, thermometers, pipe clay
triangles, droppers, measuring cylinders, fume-hoods, wire gauze, crucibles,
spectrophotometers, weighing scales, crucibles, volumetric flasks, funnels,
analytical balance, magnetic stirrer, distillation apparatus, safety goggles, etc. are
some of the basic but very essential instruments used in a laboratory.
Laboratory equipment, the measuring tools used in a scientific laboratory, often
electronic in nature. Laboratory equipment refers to the various tools and equipment
used by scientists working in a laboratory. Laboratory equipment is generally used
to either perform an experiment or to take measurements and gather data. Larger or
more sophisticated equipment is generally called a scientific instrument. Both
laboratory equipment and scientific instruments are increasingly being designed and
shared using open hardware principles. The classical equipment includes tools such
as Bunsen burners and microscopes as well as specialty equipment such as operant
conditioning chambers, spectrophotometers and calorimeters.
 6

1.Weighing Balance

A weighing balance is an instrument that is used to determine the weight or mass of

an object. It is available in a wide range of sizes with multiple weighing capacities
and is an essential tool in laboratories, commercial kitchens and pharmacies.

Principle: The principle behind weighing balances is based on the concept of

balance of weight. This means that the weight of an object is balanced against a
known weight, such as a set of calibrated weights until equilibrium is reached.
The balance then displays the weight of the object being measured.

Working:
1. Select a proper location.
1. Choose a stable and horizontal location free from external disturbances.
2. Avoid direct sunlight and make sure there are no extreme temperature changes.
3. Refrain from touching magnetic or magnetic field-generating equipment.
4. The environment should be as dust-free as possible.
 7

2. Leveling the analytical balance

1.Repeatable measurements and precise findings require precise horizontal
positioning.
2.The analytical balance must be leveled to account for any slight deviations or tilts
at this site.
3.Until the air bubble in the indicator is in the center, the analytical balance’s
leveling feet should be adjusted.
3. Calibrating the analytical balance
1.The analytical balance must be calibrated for the sample to be precisely weighed.
The following circumstances call for calibrating the operations:
•Modifications to the usage location (including moving within the same room).
•Alteration in the environment.
•Before each use.
4. Weighing
1.It is preferable to preheat it for an hour before using it.
2.Set the analytical balance to zero in the no-load condition by pressing the “tare”
button.
3.Place the weigh boat, weigh paper, or other vessel or container in the center of the
weighing pan and then shut the glass door of the weighing chamber.
4.Check the value that was displayed after it was stabilized. The appearance of the
stability mark indicates a stable state.
5.To exclude container mass from the measurement, the ‘TARE’ button is pressed to
reset the mass to zero.
6.Add the substance to be weighed after removing the container from the balance.
Avoid putting things in the balance pan because doing so can contaminate the
balance.
 8

7.Reset the container’s balance, then wait 5-10 seconds (up to a minute) for the mass
reading to stabilize.

5. Cleaning
1.Use just a piece of lint-free, soap-wet, mild detergent-coated cloth to clean the
analytical balance.
2.Avoid using any abrasive or harsh cleaning chemicals as well as organic solvents.
3.Cut off the electricity and unplug the power cord while cleaning.
4.Ensure no liquid or dust gets inside the housing of the analytical balance.
Applications
Precision and analytical balances are specific types of weighing balances which
measure much smaller masses than the average scale. Analytical balances usually
include draught proof weighing chambers for precise measuring of mass and are
often used alongside anti-vibration tables to increase accuracy.

Typically balances use a force restoration mechanism that when a force is applied
(i.e. a load or weight), the balance counteracts this force exerted from the
unknown mass. Balances are generally more sophisticated and precise than scales
and are therefore commonly used by professionals for advanced scientific
weighing in the aforementioned industries.

Due to their high precision and advanced technology, precision and analytical
balances are used specifically in laboratories in order to efficiently perform tasks
such as weighing test materials and sampling amounts, formulation, density
determination, purity analysis, quality control testing and material and
conformance testing. Balances with higher capacities are not only used in
laboratories but can be used to test larger high-capacity weighing materials such
as in construction sites.
 9

2.Rotary Evaporator

A rotary evaporator (also called as “rotavap” or “rotovap”) is a device used in labs for
the efficient and gentle removal of solvents from samples by evaporationRotary
evaporation is the process of reducing the volume of a solvent by distributing it as a
thin film across the interior of a vessel at elevated temperature and reduced pressure.
This promotes the rapid removal of excess solvent from less volatile samples. Most
rotary evaporators have four major components: heat bath, rotor, condenser, and
solvent trap. Additionally, an aspirator or vacuum pump needs to be attached, as well as
a bump trap and round bottom flask containing the sample to be concentrated.

Principle: Rotary evaporators work on the principle that solvents have a range of
boiling points, which decrease under reduced pressure. The evaporation flask rotates
at a specified speed forcing the materials to form a large area of thin film on the
inner wall of the flask.

Working: Rotary evaporators are also used for concentration, crystallization, drying,
separation, and solvent recovery in addition to the continuous distillation of volatile
solvents and are utilized in various fields and applications, including pharmaceutical,
chemical, and biotechnology industries.
 10

 The flask is heated evenly, and materials with a lower boiling point rapidly
evaporate.
 Recycling of the solvent stream occurs in the receiving flask, following cooling
by the glass condenser.
 Users can carry out solvent removal faster and more efficiently than
evaporation under atmospheric pressure, thus saving time and increasing
productivity in the laboratory.
 In part, this accelerated evaporation is due to the film’s formation on the flask’s
inner surface, which increases evaporation significantly.
 It is therefore relatively quick to achieve solvent removal (depending on
volume and solvent).
 Rotary evaporators are simple to use and are commonly found in laboratories.

Factors important when selecting a rotary evaporator:

One of the most critical considerations for rotary evaporator selection is solvent type.
Understanding the properties of solvent is beneficial as it informs the user about the
total vacuum required. Solvent boiling points decrease substantially when under
vacuum, for example:
Solvent Boiling Point at 1 mbar Boiling Point at 53 mbar
 11

Acetonitrile 81°C 7.7°C

Ethanol 78.4°C 19°C

Monitoring low boiling points is essential so that the bath temperature does not exceed
these temperatures.
It is vital to consider heating and cooling capacity. The temperature difference between
the solvent solution and the condenser must be sufficient. Typically, the condenser is
cooled using dry ice or circulated tap water, but recirculated chillers can be used and
are beneficial because they are less labor-intensive to use. Circulators are greener, save
water, and, over a period of time, more cost-effective. They also prevent potential
laboratory floods.
Tailoring automation and accessories can ensure streamlined workflow when using
rotary evaporators. Certain automated features such as motorized lifts and automatic
boiling point detection can minimize operational time.
Applications:
As an essential separation equipment, a rotary evaporator can remove a volatile
solvent from a liquid mixture through evaporation and condensation. In industrial
field, people use rotary evaporators to extract cbd, which is the main component of
marijuana. And cbd is usually used to be made into medicine in pharmaceutical
field.
It is synonymous with cutting-edge technology and even psychology. The use of a
rotary evaporator to non-heat evaporate liquid, thus retaining volatile aromatics that
are easily lost by heating, is a perfect combination of modern culinary and
experimental instruments.

3.Parallel Synthesizer
 12

Parallel synthesis enables substantial time savings and compound differentiation by

running multiple experiments simultaneously. Parallel synthesis is used to accelerate
the discovery of new compounds and to screen for optimal process conditions.
Principle: In a parallel synthesis method, individual peptides are synthesized in
separate reaction vessels, and this defines the sequence of a peptide based on the
location of a particular reaction vessel.
Working:
1. The reagents are prepared and loaded into the system along with appropriate
reaction conditions.
2. Parallel synthesizers enable the rapid synthesis and screening of a large number of
compounds, accelerating research and development processes.
3. Parameters such as temperature, pressure, stirring speed, and reaction time are
controlled and monitored for each reaction vessel individually or as a group.
4. A hot plate in parallel synthesizers provides controlled heating to the reaction
vessels.5. Sensors monitor the temperature in each reaction vessel, ensuring that
reactions are conducted at the desired temperature and enabling temperature
control systems to make adjustments as needed.
 13

6. Parallel synthesizers often have gas connections to introduce gases into the
reaction vessels.
7. The reactions are initiated and allowed to proceed for a specific time duration.
8. Data from multiple reactions are processed and analyzed to identify promising
compounds or optimize reaction conditions.
9. Parallel synthesizers are quick to set up an easy to use.
Applications
These systems provide high throughput screening and saves on time and
space, helps in comparative studies, and assists in faster and advanced
research. These parallel synthesizers are often used for high throughput
catalyst screening. These multiple autoclave systems are used in
Laboratories, pilot facility & small-scale manufacturing of fine &
specialty chemicals, bulk drug (API) pharmaceuticals, dyes, intermediates,
paints, oils, agrochemical, petrochemicals, oil & gas, chemical engineering
colleges / research institutes / defense organizations etc. to carry out
various high pressure high temperature liquid-liquid, gas-liquid and gas-
liquid-solid reactions like Alkylation, amination, acetylation, acylation,
bromination, carboxylation, catalytic reduction, chlorination,
dehydrogenation, esterification, ethoxylation, halogenation,
hydrogenation, methylation, nitration, oxidation, ozonization,
polymerization, sulphonation etc. These reactors are used to invent new
molecules / chemicals & study reaction parameters, for organic synthesis,
for reaction calorimetry to study heat of reaction.
 14

4. Fume Hood

A fume hood is an enclosure that safely contains and ventilates hazardous fumes,
vapors, gases and dust generated by chemical processes performed in the fume
hood. Sometimes called a chemical hood or a lab hood, a fume hood protects
workers from inhalation of hazardous substances.

The clear sliding window on a fume hood, called the sash, also shields workers
from spills and splashes that may occur in the chemical fume hood.

Fume hoods are the workhorse of laboratory exhaust systems and are the most
widely used approach for local ventilation.

Principle: The functions of a fume hood are as follows:

 To protect the user from inhaling toxic fumes

 To protect the experiment or sample from contamination
 To protect the user from explosions or spills
 15

To achieve the above, a fume hood has three main parts ‒ the table, the enclosure,
and the system.

The table is generally a standard CRCA made C-frame or H-Frame work, with
under-table storage like shuttered cabinets and/or drawers, where you can keep
some lab equipment. The enclosure also is CRCA-made; with a glass shutter at one
side. The glass in the shutter should be of good quality ‒ some advanced models
may even be explosion-proof.

Working:
1. A fume hood has a ventilation system that includes an exhaust fan and ductwork
which creates negative pressure inside the fume hood, drawing air and
contaminants into the hood.
2. Fume hoods are designed with sash (movable transparent panel) at the front,
which can be raised or lowered. Blower located on the roof or outside the
building and is responsible for creating the airflow that pulls air through the
hood.
3. Inside the fume hood, various laboratory procedures can be conducted safely,
such as chemical reactions, handling hazardous materials, or working with
volatile substances.
4. A magnetic beat in RB with a heating block is a common laboratory instrument
used for mixing and heating solutions simultaneously.
5. Heating block is equipped with a heating element that can be controlled to raise
the temperature of the solutions.
 16

Applications

This does not apply to highly toxic and toxic compressed gases, in cylinders large
than 20ft3 at STP due to the face velocity requirements.

 The smallest possible cylinder should be used for the experiment (a six-
month bottle supply for routine use gases is appropriate, while smaller
cylinder supplies are suggested for short term use);

 Cylinders of toxic and highly toxic gases that are 20 ft3 or smaller at NTP
are allowed within fume hoods as long as there are no incompatible
materials also used in the hood or storage of any items inside.

 Make an effort to obtain gas cylinders in returnable bottles;

 Order bottles with lowest cylinder pressure possible;

 Use a flow restricting orifice or needle valve to restrict flow to only that
needed for the experiment;
 17

5. Soxhlet Apparatus

A Soxhlet extractor is a piece of laboratory apparatus invented in 1879 by Franz von

Soxhlet. It was originally designed for the extraction of a lipid from a solid material.
Typically, Soxhlet extraction is used when the desired compound has
a limited solubility in a solvent, and the impurity is insoluble in that solvent. It
allows for unmonitored and unmanaged operation while efficiently recycling a small
amount of solvent to dissolve a larger amount of material.
Description
A Soxhlet extractor has three main sections: a percolator (boiler and reflux) which
circulates the solvent, a thimble (usually made of thick filter paper) which retains
the solid to be extracted, and a siphon mechanism, which periodically empties the
condensed solvent from the thimble back into the percolator.
 18

Assembly

 The source material containing the compound to be extracted is placed inside

the thimble.

 The thimble is loaded into the main chamber of the Soxhlet extractor.
 The extraction solvent to be used is placed in a distillation flask.
 The flask is placed on the heating element.
 The Soxhlet extractor is placed atop the flask.
 A reflux condenser is placed atop the extractor.

Working
 The solvent is heated to reflux. The solvent vapor travels up
a distillation arm, and floods into the chamber housing the thimble of solid.
 The condenser ensures that any solvent vapor cools, and drips back down
into the chamber housing the solid material.
 19

 The chamber containing the solid material slowly fills with warm solvent.
Some of the desired compound dissolves in the warm solvent. When the
Soxhlet chamber is almost full, the chamber is emptied by the siphon. The
solvent is returned to the distillation flask.
 The thimble ensures that the rapid motion of the solvent does not transport
any solid material to the still pot. This cycle may be allowed to repeat many
times, over hours or days.
 During each cycle, a portion of the non-volatile compound dissolves in the
solvent. After many cycles the desired compound is concentrated in the
distillation flask. The advantage of this system is that instead of many
portions of warm solvent being passed through the sample, just one batch of
solvent is recycled.
 After extraction the solvent is removed, typically by means of a rotary
evaporator, yielding the extracted compound. The non-soluble portion of the
extracted solid remains in the thimble, and is usually discarded.
 Like Soxhlet extractor, the Kumagawa extractor has a specific design where
the thimble holder/chamber is directly suspended inside the solvent flask
(having a vertical large opening) above the boiling solvent.
 The thimble is surrounded by hot solvent vapor and maintained at a higher
temperature compared to the Soxhlet extractor, thus allowing better
extraction for compounds with higher melting points such as bitumen.
 The removable holder/chamber is fitted with a small siphon side arm and, in
the same way as for Soxhlet, a vertical condenser ensures that the solvent
drips back down into the chamber which is automatically emptied at every
cycle.
 20

UV-visible and IR Spectroscopy

1.Ultraviolet-visible Spectroscopy (UV-vis)

Ultraviolet-visible spectroscopy or ultraviolet-visible spectrophotometry (UV-Vis or
UV/Vis) refers to absorption spectroscopy or reflectance spectroscopy in the
ultraviolet-visible spectral region. Ultraviolet-visible (UV-VIS) spectroscopy is an
analytical method that can measure the analyte quantity depending on the amount of
light received by the analyte.

Principle: The Principle of UV-Visible Spectroscopy is based on the absorption of

ultraviolet light or visible light by chemical compounds, which results in the
production of distinct spectra. Spectroscopy is based on the interaction between
light and matter.
 21

Instrumentation:
 A UV-Vis spectrophotometer consists of a light source, a monochromator, a
detector, and a data recorder.
 The light source provides illumination at one or more specific wavelengths.
 The monochromator is used to select the wavelength of light that passes
through the sample.
 The detector measures the intensity of the light that passes through the sample.
 The data recorder records the absorbance or transmission of light at each
wavelength.

Parts of UV-Vis Spectroscopy

Light Source
 Tungsten filament lamps and Hydrogen-Deuterium lamps are the most widely
used and suitable light sources as they cover the whole UV region.
 Tungsten filament lamps are rich in red radiations; more specifically they emit
the radiations of 375 nm, while the intensity of Hydrogen-Deuterium lamps falls
below 375 nm.
 22

Monochromator
 Monochromators generally are composed of prisms and slits.
 Most of the spectrophotometers are double beam spectrophotometers.
 The radiation emitted from the primary source is dispersed with the help of
rotating prisms.
 The beam selected by the slit is monochromatic and further divided into two
beams with the help of another prism.
Sample and reference cells
 One of the two divided beams is passed through the sample solution and the
second beam is passé through the reference solution.
 Both sample and reference solution is contained in the cells.
 These cells are made of either silica or quartz. Glass can’t be used for the cells as
it also absorbs light in the UV region.
Detector
 Generally, two photocells serve the purpose of the detector in UV spectroscopy.
 One of the photocells receives the beam from the sample cell and the second
detector receives the beam from the reference.
 The intensity of the radiation from the reference cell is stronger than the beam of
the sample cell. This results in the generation of pulsating or alternating currents
in the photocells.
Amplifier
 The alternating current generated in the photocells is transferred to the amplifier.
 The amplifier is coupled to a small servometer.

Recording devices
 Most of the time amplifier is coupled to a pen recorder which is connected to the
computer.
 23

 The computer stores all the data generated and produces the spectrum of the
desired compound.

Applications of UV Spectroscopy
Detection of Impurities
 It is one of the best methods for the determination of impurities in organic
molecules.
 Additional peaks can be observed due to impurities in the sample and it can be
compared with that of standard raw material.
 By also measuring the absorbance at a specific wavelength, the impurities can be
detected.
 24

Structure elucidation of organic compounds

It is useful in the structure elucidation of organic molecules, such as in detecting
the presence or absence of unsaturation, the presence of heteroatoms.
1. UV absorption spectroscopy can be used for the quantitative determination of
compounds that absorb UV radiation.
2. UV absorption spectroscopy can characterize those types of compounds that
absorb UV radiation thus used in the qualitative determination of compounds.
Identification is done by comparing the absorption spectrum with the spectra of
known compounds.
3. This technique is used to detect the presence or absence of a functional group in
the compound. The absence of a band at a particular wavelength is regarded as
evidence for the absence of particular group.
4. Kinetics of reaction can also be studied using UV spectroscopy. The UV
radiation is passed through the reaction cell and the absorbance changes can be
observed.
 25

Infra-Red Spectroscopy (IR)

Infrared (IR) spectroscopy or vibrational spectroscopy is an analytical technique
that takes advantage of the vibrational transitions of a molecule.
It is one of the most common and widely used spectroscopic techniques
employed mainly by inorganic and organic chemists due to its usefulness in
determining the structures of compounds and identifying them.
The method or technique of infrared spectroscopy is conducted with an instrument
called an infrared spectrometer to produce an infrared spectrum.
Principle:
1. Infrared Spectroscopy is the analysis of infrared light interacting with a
molecule.
2. The portion of the infrared region most useful for analysis of organic compounds
have a wavelength range from 2,500 to 16,000 nm, with a corresponding
frequency range from 1.9*1013 to 1.2*1014 Hz.
3. Photon energies associated with this part of the infrared (from 1 to 15 kcal/mole)
are not large enough to excite electrons, but may induce vibrational excitation of
covalently bonded atoms and groups.
4. It is known that in addition to the facile rotation of groups about single bonds,
molecules experience a wide variety of vibrational motions, characteristic of their
component atoms.
5. Consequently, virtually all organic compounds will absorb infrared radiation that
corresponds in energy to these vibrations.
6. Infrared spectrometers, similar in principle to other spectrometer, permit
chemists to obtain absorption spectra of compounds that are a unique reflection
of their molecular structure.
 26

7. The fundamental measurement obtained in infrared spectroscopy is an infrared

spectrum, which is a plot of measured infrared intensity versus wavelength (or
frequency) of light.
 IR Spectroscopy measures the vibrations of atoms, and based on this it is
possible to determine the functional groups.
 Generally, stronger bonds and light atoms will vibrate at a high stretching
frequency (wavenumber).

Instrumentation of IR Spectroscopy
The main parts of the IR spectrometer are as follows:
1. Radiation source
2. Sample cells and sampling of substances
3. Monochromators
4. Detectors
5. Recorder
 27

IR Radiation Sources
IR instruments require a source of radiant energy which emits IR radiation which
must be steady, intense enough for detection, and extend over the desired
wavelength.
Various sources of IR radiations are as follows.
1. Nernst glower
2. Incandescent lamp
3. Mercury arc
4. Tungsten lamp
5. Glober source
6. Nichrome wire

Sample cells and sampling of substances

IR spectroscopy has been used for the characterization of solid, liquid, or gas
samples.
i. Solid – Various techniques are used for preparing solid samples such as pressed
pellet technique, solid run in solution, solid films, mull technique, etc.
 28

ii. Liquid – Samples can be held using a liquid sample cell made of alkali halides.
Aqueous solvents cannot be used as they will dissolve alkali halides. Only organic
solvents like chloroform can be used.
iii. Gas– Sampling of gas is similar to the sampling of liquids.
Monochromators
 Various types of monochromators are prism, gratings and filters.
 Prisms are made of Potassium bromide, Sodium chloride or Cesium iodide.
 Filters are made up of Lithium Fluoride and Diffraction gratings are made up of
alkali halides.
Detectors
 Detectors are used to measure the intensity of unabsorbed infrared radiation.
 Detectors like thermocouples, Bolometers, thermistors, Golay cell, and pyro-
electric detectors are used.
Recorders
 Recorders are used to record the IR spectrum.
Applications of Infra-Red Spectroscopy
It has been of great significance to scientific researchers in many fields such as:
 Protein characterization
 Nanoscale semiconductor analysis and
 Space exploration.
 Analysis of gaseous, liquid or solid samples
 Identification of compounds
 Quantitative analysis
 Information regarding functional groups of molecules and constitution of
molecules can be deduced from IR spectrum
 To know about interaction among molecules
 29

Gas Chromatography

 Gas chromatography differs from other forms of chromatography in that the

mobile phase is a gas and the components are separated as vapors.
 It is thus used to separate and detect small molecular weight compounds in the
gas phase.
 The sample is either a gas or a liquid that is vaporized in the injection port. The
mobile phase for gas chromatography is a carrier gas, typically helium because of
its low molecular weight and being chemically inert.
 The pressure is applied and the mobile phase moves the analyte through the
column. The separation is accomplished using a column coated with a stationary
phase.
 30

Principle
The equilibrium for gas chromatography is partitioning, and the components of the
sample will partition (i.e. distribute) between the two phases: the stationary phase
and the mobile phase.
Compounds that have a greater affinity for the stationary phase spend more time in
the column and thus elute later and have a longer retention time (Rt) than samples
that have a higher affinity for the mobile phase.
Affinity for the stationary phase is driven mainly by intermolecular interactions
and the polarity of the stationary phase can be chosen to maximize interactions and
thus the separation.
Ideal peaks are Gaussian distributions and symmetrical, because of the random
nature of the analyte interactions with the column.
 The separation is hence accomplished by partitioning the sample between the gas
and a thin layer of a nonvolatile liquid held on a solid support.
 A sample containing the solutes is injected into a heated block where it is
immediately vaporized and swept as a plug of vapor by the carrier gas stream
into the column inlet.
 The solutes are adsorbed by the stationary phase and then desorbed by a fresh
carrier gas.
 The process is repeated in each plate as the sample is moved toward the outlet.
 Each solute will travel at its own rate through the column.
 Their bands will separate into distinct zones depending on the partition
coefficients, and band spreading.
 The solutes are eluted one after another in the increasing order of their kd, and
enter into a detector attached to the exit end of the column.
 31

 Here they register a series of signals resulting from concentration changes and
rates of elution on the recorder as a plot of time versus the composition of carrier
gas stream.
 The appearance time, height, width, and area of these peaks can be measured to
yield quantitative data.

Parts of Gas chromatography

Gas chromatography is mainly composed of the following parts:
1. Carrier gas in a high-pressure cylinder with attendant pressure
regulators and flow meters
 Helium, N2, H, Argon are used as carrier gases.
 Helium is preferred for thermal conductivity detectors because of its high thermal
conductivity relative to that of most organic vapors.
 N2 is preferable when a large consumption of carrier gas is employed.
 Carrier gas from the tank passes through a toggle valve, a flow meter, (1-1000
ml/min), capillary restrictors, and a pressure gauge (1-4 atm).
 Flow rate is adjusted by means of a needle valve mounted on the base of the flow
meter and controlled by capillary restrictors.
 The operating efficiency of the gas chromatograph is directly dependant on the
maintenance of constant gas flow.
2. Sample injection system
 Liquid samples are injected by a microsyringe with a needle inserted through a
self-scaling, silicon-rubber septum into a heated metal block by a resistance
heater.
 Gaseous samples are injected by a gas-tight syringe or through a by-pass loop
and valves.
 32

 Typical sample volumes range from 0.1 to 0.2 ml.

3. The separation column
 The heart of the gas chromatography is the column which is made of metals bent
in U shape or coiled into an open spiral or a flat pancake shape.
 Copper is useful up to 2500
 Swage lock fittings make column insertion easy.
 Several sizes of columns are used depending upon the requirements.
4. Liquid phases
 An infinite variety of liquid phases are available limited only by their volatility,
thermal stability and ability to wet the support.
 No single phase will serve for all separation problems at all temperatures.
Non-Polar – Paraffin, squalene, silicone greases, apiezon L, silicone gum rubber.
These materials separate the components in order of their boiling points.
Intermediate Polarity – These materials contain a polar or polarizable group on a
long non-polar skeleton which can dissolve both polar and non-polar solutes. For
example, diethyl hexyl phthalate is used for the separation of high boiling alcohols.
Polar – Carbowaxes – Liquid phases with a large proportion of polar groups.
Separation of polar and non-polar substances.
Hydrogen bonding – Polar liquid phases with high hydrogen bonding e.g. Glycol.
Specific purpose phases – Relying on a chemical reaction with solute to achieve
separations. e.g. AgNO3 in glycol separates unsaturated hydrocarbons.
5. Supports
 The structure and surface characteristics of the support materials are important
parameters, which determine the efficiency of the support and the degree of
separation respectively.
 33

 The support should be inert but capable of immobilizing a large volume of liquid
phase as a thin film over its surface.
 The surface area should be large to ensure the rapid attainment of equilibrium
between stationary and mobile phases.
 Support should be strong enough to resist breakdown in handling and be capable
of packed into a uniform bed.
 Diatomaceous earth, kieselguhr treated with Na 2CO 3 for 9000 C causes the
particle fusion into coarser aggregates.
 Glass beads with a low surface area and low porosity can be used to coat up to
3% stationary phases.
 Porous polymer beads differing in the degree of cross-linking of styrene with
alkyl-vinyl benzene are also used which are stable up to 2500
6. Detector
 Detectors sense the arrival of the separated components and provide a signal.
 These are either concentration-dependent or mass dependent.
 The detector should be close to the column exit and the correct temperature to
prevent decomposition.
7. Recorder
 The recorder should be generally 10 mv (full scale) fitted with a fast response
pen (1 sec or less). The recorder should be connected with a series of good
quality resistances connected across the input to attenuate the large signals.
 An integrator may be a good addition.
 34

Step 1: Sample Injection and Vaporization

1. A small amount of liquid sample to be analyzed is drawn up into a syringe.
2. The syringe needle is positioned in the hot injection port of the gas
chromatograph and the sample is injected quickly.
3. The injection of the sample is considered to be a “point” in time, that is, it is
assumed that the entire sample enters the gas chromatograph at the same time, so
the sample must be injected quickly.
4. The temperature is set to be higher than the boiling points of the components of
the mixture so that the components will vaporize.
5. The vaporized components then mix with the inert gas mobile phase to be carried
to the gas chromatography column to be separated.
Step 2: Separation in the Column
 Components in the mixture are separated based on their abilities to adsorb on or
bind to, the stationary phase.
 A component that adsorbs most strongly to the stationary phase will spend the
most time in the column (will be retained in the column for the longest time) and
 35

will, therefore, have the longest retention time (Rt). It will emerge from the gas
chromatograph last.
 A component that adsorbs the least strongly to the stationary phase will spend the
least time in the column (will be retained in the column for the shortest time) and
will, therefore, have the shortest retention time (Rt). It will emerge from the gas
chromatograph first.
 If we consider a 2 component mixture in which component A is more polar than
component B then:
1. component A will have a longer retention time in a polar column than component
B
2. component A will have a shorter retention time in a non-polar column than
component B

Step 3: Detecting and Recording Results

1. The components of the mixture reach the detector at different times due to
differences in the time they are retained in the column.
2. The component that is retained the shortest time in the column is detected
first. The component that is retained the longest time in the column is detected
last.
3. The detector sends a signal to the chart recorder which results in a peak on the
chart paper. The component that is detected first is recorded first. The
component that is detected last is recorded last.
Applications
 GC analysis is used to calculate the content of a chemical product, for example in
assuring the quality of products in the chemical industry; or measuring toxic
substances in soil, air or water.
 36

 Gas chromatography is used in the analysis of:

(a) air-borne pollutants
(b) performance-enhancing drugs in athlete’s urine samples
(c) oil spills
(d) essential oils in perfume preparation
 GC is very accurate if used properly and can measure picomoles of a substance in
a 1 ml liquid sample, or parts-per-billion concentrations in gaseous samples.
 Gas Chromatography is used extensively in forensic science. Disciplines as
diverse as solid drug dose (pre-consumption form) identification and
quantification, arson investigation, paint chip analysis, and toxicology cases,
employ GC to identify and quantify various biological specimens and crime-
scene evidence.
Advantages
 The use of longer columns and higher velocity of carrier gas permits the fast
separation in a matter of a few minutes.
 Higher working temperatures up to 5000C and the possibility of converting any
material into a volatile component make gas chromatography one of the most
versatile techniques.
 GC is popular for environmental monitoring and industrial applications because
it is very reliable and can be run nearly continuously.
 GC is typically used in applications where small, volatile molecules are detected
and with non-aqueous solutions.
 GC is favored for non-polar molecules.
 37

IPR (Intellectual Property Rights)

Intellectual Property Rights (IPRs) are the rights associated with intangible property
owned by a person/company and protected against use without consent. Thus,
rights relating to ownership of intellectual property are called Intellectual
Property Rights. These rights aim to protect intellectual property (creations of
human intellect) by allowing the creators of trademarks, patents, or copyrighted
works to benefit from their creations. The Universal Declaration of Human
Rights (UDHR) also refers to intellectual property rights under Article 27 which
states that “Everyone has the right to the protection of the moral and material
interests resulting from any scientific, literary or artistic production of which
he is the author.”
Thus, the purpose of IPR is to reward human intellect by providing exclusive rights
to the creators over their inventions, artistic, musical works, etc.

In this article, the author has discussed the meaning of intellectual property and
intellectual property rights, the international regime of IPR and laws relating to
IPR in India, etc.

Meaning and nature of the intellectual property

Intellectual property (IP) is an intangible property that comes into existence

through human intellect. It refers to the creations of the mind or the products of
human intellect such as inventions; designs; literary and artistic works; symbols,
names and images used in commerce.

The “Convention Establishing the World Intellectual Property Organization” states

that “intellectual property” shall include the rights relating to: —
 38

1. Literary, artistic, and scientific works,

2. Performances of performing artists, phonograms, and broadcasts,

3. Inventions in all fields of human endeavor,

4. Scientific discoveries,

5. Industrial designs,

6. Trademarks, service marks, commercial names and designations,

7. Protection against unfair competition, and

8. All other rights resulting from intellectual activity in the industrial,

scientific, literary, or artistic fields.
Other categories of intellectual property include geographical indications, rights in
respect of know-how or undisclosed information, and layout designs of integrated
circuits.

Meaning of Intellectual Property Rights

The term “Intellectual Property Rights (IPR)” is used to refer to the bundle of
rights conferred by law on a creator/owner of intellectual property. These are the
rights that a person has over the creations of his mind. The creators and inventors
are thus allowed to benefit from their creations. IP rights are the legal rights
governing the use of intellectual property.
 39

Need for legal protection of intellectual property

The various reasons behind granting protection to intellectual property through the
enactment of suitable Intellectual Property (IP) laws are as follows:

1. To encourage inventions and creations that promote the social, economic,

scientific, and cultural development of society by incentivizing the
creators and allowing them to make economic gains out of their creations.

2. To provide legal protection to intellectual creations.

3. To prevent third parties from enjoying the fruits of someone else’s

creativity.

4. To facilitate fair trading.

5. To promote creativity and its dissemination.

6. Giving recognition to the efforts of creators.

7. Preventing the infringement of proprietary rights of creators in their

creations from unauthorized use.

8. To encourage investment of skill, time, finance, and other resources into

innovation activities in a manner that is beneficial to society.
 40

Advantages and disadvantages of Intellectual Property Rights

Advantages of Intellectual Property Rights

1. IPR protection gives your business a competitive advantage over other

similar businesses.

2. IPR protection allows you to prevent unauthorized use of your intellectual

property and works.

3. IPR enhances the value of your company and also opens avenues for
collaborations and opportunities for generating income such as by
entering into licensing agreements to exploit/work the invention/work.

4. IPR helps to attract clients and creates your brand value. For example, the
consumers start identifying your products with the unique logo or
registered trademark.

Disadvantages of Intellectual Property Rights

1. You have to incur additional costs for getting IPR protection including
legal costs and other fees.

2. Even after getting the intellectual property right, you might still face a lot
of difficulties in curbing the copying and unauthorized use of your work.
Moreover, sometimes an attempt to enforce IP rights could lead to a
reduction in the consumer base.

3. IP rights aren’t absolute. There are certain limitations and conditions

imposed by law on the exercise of these rights (such as a limited period of
 41

protection and compulsory licensing provisions) in the interests of the

general public.

Components of Intellectual Property Rights

Copyright

The term ‘copyright’ concerns the rights of the creators/authors of literary and
artistic works. A copyright is also called a ‘literary right’ or ‘author’s right’.
Copyright gives an author exclusive rights to his creation and prevents the copying
and unauthorized publishing of his work. Copyright protection begins at the very
moment a work is created and expressed in some tangible form. Copyright
protection is granted to a work that is an original creation. Also, the protection
extends only to expressions. Copyright protects the following two rights of the
author:

1. Economic rights i.e., the right of the owner to derive financial benefit
from the use of their works by others. For instance, the right to prohibit or
authorize reproduction of the work in various forms, the right to prohibit
unauthorized translation of the work, etc.

2. Moral rights i.e., protection of non-economic interests of the author. For

instance, the right to oppose changes to work and the right to claim
authorship, etc.

What kind of works can be protected under copyright?

The following categories of works typically come under copyright protection:

 42

 Literary works such as novels, plays, poems, and newspaper articles;

 Computer programs and databases;

 Films, musical compositions, and choreography;

 Architecture and advertisements, maps, and technical drawings.

In India, the term of copyright protection extends throughout the lifetime of the
author and then 60 years after his death.

Law relating to copyright in India: The Copyright Act, 1957

The Copyright Act, 1957 is a comprehensive legislation dealing with copyrights in

India. The Act regulates the various aspects relating to copyright regime in India
such as:

 Registration of copyright

 Publication, term of copyright

 Assignment, and license of copyright

 Special rights of broadcasting organization and performer’s rights

 Infringement of copyright and remedies thereof

 Establishment of copyright authorities and copyright societies

 International Copyright
The term of copyright protection provided under the Act for the various categories
of works is given below:

1. Literary, dramatic, musical and artistic works: Life of the author plus 60
years after death.
 43

2. Anonymous and pseudonymous works: 60 years from the date of

publication. However, if the identity of the author is disclosed before the
expiry of that 60 years, then the term of protection shall be life of the
author plus 60 years after death.

3. Posthumous works: 60 years from publication.

4. Cinematograph films: 60 years from publication.

5. Sound recordings: 60 years from publication.

6. Government work: 60 years from publication.

7. Works of public undertakings: 60 years from publication.

8. Works of international organizations: 60 years from the publication of the

work.

Copyright infringement

Section 51 of the Copyright Act, 1957 provides for ‘What constitutes copyright
infringement’. Copyright is said to be infringed:

1. when a person does something that the owner of the copyright has the
exclusive right to do, or permits for profit the use of any place for the
purpose of the communication of the work to the public, where such
communication constitutes an infringement of the copyright in the work,
without a licence or in violation of the conditions of the licence.

2. When any person makes for sale or hire, sells or lets for hire, or displays
or offers for sale or hire, or distributes either for the purpose of trade or to
 44

such an extent as to prejudice the owner of the copyright, or exhibits in

public, or imports into India any infringing copies of the work.
Section 52 enlists the acts which do not constitute an infringement of copyright
such as fair dealing in any work for personal, private use or for research,
reproducing any work for the purpose of a judicial proceeding or replication by a
teacher or a pupil in the course of teaching etc.

It is pertinent to note that the Copyright Act provides for both civil and criminal
remedies against infringement of copyright.

Types of IPR

Patents

A patent is an exclusive right granted for an invention or innovation, which might

be a product, a method or a process, that introduces a novel way of doing
something or offers a new technical solution to a problem. In other words, it is a
right of monopoly granted to a person who has invented:
 45

1. a new and useful article, or

2. improvement of an existing article, or

3. a new process of making an article.

A patent is granted for inventions having industrial and commercial value. It is the
exclusive right to manufacture the new article/manufacture the article with the
invented process for a limited period of time (usually 20 years from the filing
date of the application) in exchange for disclosure of the invention. A patent
owner can sell his patent or grant licence to others to exploit the same.

Trademarks and service marks

A trademark is a symbol that is used to distinguish the goods of one enterprise
from its competitors. A trademark may consist of a single letter, logo, symbol,
design, or numerals and three-dimensional features such as shape and packaging,
etc. Section 2(zb) of the Trademarks Act, 1999 defines “trademark” as a mark
capable of graphical representation and which can be used to distinguish the goods
or services of one person from those of others. A trademark may include the shape
of goods, their packaging, and a combination of colors. Hence, distinctiveness is
the hallmark of a trademark.

Trademarks used in connection with services such as tourism, banking, etc., are
called Service Marks.

The owner has the exclusive right to the use of a registered trademark. There are
45 classes of trademarks, consisting of 34 classes of products and 11 classes for
services.
 46

Industrial designs

An industrial design means the ornamental or visual aspects of an article. It may

consist of three-dimensional features, for instance, the shape of an article, or two-
dimensional features, such as lines, patterns, or color. An industrial design is
purely aesthetic, non-functional, and has no utility. It is necessary to provide legal
protection to the creative originality of an industrial design to prevent others from
copying it.

Geographical Indications (GI)

A geographical indication (GI) is used to identify goods having a specific

geographical origin. These indications denote quality, reputation, or other
characteristics of such goods essentially attributable to their geographical origin.
Generally, geographical indications are used for foodstuffs, agricultural products,
wine, industrial products and handicrafts. Examples of GI include Basmati Rice,
Darjeeling Tea etc.

Trade Secrets

Trade Secrets are IP rights on confidential information which may be sold or

licensed. A trade secret refers to any confidential business information and may
include designs, drawings, plans, business strategies, R & D related information,
etc. In order to qualify as a trade secret, the information should be commercially
valuable i.e. useful in a trade or business, known to a small number of people, and
subject to reasonable steps taken by the rightful holder of the information to keep it
secret.
 47

Layout designs of integrated circuits

Integrated circuits are used in products such as television, radio, mobile, washing
machine, and data processing instruments. The layout designs of integrated circuits
not only reduce the space but also enhance the capacity and performance of the
system. In India, the Semiconductor Integrated Circuit Layout Design Act,
2000 regulates the registration, use, and protection of original and distinct layout
designs.
 48

Basic Techniques

Crystallization

Crystallization is a technique used for the purification of substances. A separation

technique to separate solids from a solution.

Crystallization can be defined as the process through which the atoms/molecules of

a substance arrange themselves in a well-defined three-dimensional lattice and
consequently, minimize the overall energy of the system. When a substance is
subjected to crystallization, its atoms or molecules bind together through well-
defined angles.

Distillation

Distillation refers to the selective boiling and subsequent condensation of a

component in a liquid mixture. It is a separation technique that can be used to
 49

either increase the concentration of a particular component in the mixture or to

obtain (almost) pure components from the mixture. The process of distillation
exploits the difference in the boiling points of the components in the liquid mixture
by forcing one of them into a gaseous state.

It is important to note that distillation is not a chemical reaction but it can be

considered as a physical separation process.

Solvent Extraction

Solvent extraction is the separation of a particular substance from a mixture by

dissolving that substance in a solvent that will dissolve it, but which will not
dissolve any other substance in the mixture. The solution containing the desired
metal is mixed with an appropriate solvent and the metal is extracted, in a process
of solvent extraction. In solvent extraction, a substance is treated with a solvent
and the substance separates into more and less soluble components.
 50

Column Chromatography

Column Chromatography is a preparative technique used to purify compounds

depending on their polarity or hydrophobicity. In column chromatography, a
mixture of molecules is separated based on their differentials partitioning between
a mobile phase and a stationary phase.

Thin Layer Chromatography

Thin-layer chromatography (TLC) is a chromatography technique that separates

components in non-volatile mixtures.
 51

It is performed on a TLC plate made up of a non-reactive solid coated with a thin

layer of adsorbent material. This is called the stationary phase. The sample is
deposited on the plate, which is eluted with a solvent or solvent mixture known as
the mobile phase (or eluent). This solvent then moves up the plate via capillary
action. As with all chromatography, some compounds are more attracted to the
mobile phase, while others are more attracted to the stationary phase. Therefore,
different compounds move up the TLC plate at different speeds and become
separated. To visualize colorless compounds, the plate is viewed under UV light or
is stained. Testing different stationary and mobile phases is often necessary to
obtain well-defined and separated spots.

Physical determination of Organic Compounds

Boiling Point

The boiling point of organic compounds depends on their molecular weight. As the
molecular weight increases, so does the boiling point. For two compounds of the
same molecular weight, various factors determine the boiling point of an organic
compound.

Melting Point

The melting point of an organic solid can be determined by introducing a tiny

amount into a small capillary tube, attaching this to the stem of a thermometer
placed in the center in a heating bath, heating the bath slowly, and observing the
temperatures at which melting begins and is complete.
 52

Pharma Industry and APIs

What are APIs?

Active pharmaceutical ingredients (APIs) are the chemical-based compounds that

have produced mainly in the countries the USA, Europe, China, and India. APIs
have pharmacological activity mainly used with combination of other ingredients
to diagnose, cure, mitigate, and treat the disease. However, in the recent past years,
many medicinal-based corporations have started importing these substances from
countries producing active ingredients to their home countries. Modern day
medicines have been used by people to prevent, treat, diagnose, and cure disease.
Every single medication is composed of two main components, i.e. the API, which
is the major component, is chemically and biologically active that has to do the
work in your body and other component known as excipients like lactose or
mineral oil in the pill, which is chemically inactive that provides, e.g. volume, a
sweet flavor, or a color. These excipients help in the delivery of APIs in the body
system. Numerous chemical compounds and raw materials are utilized in multi-
step reaction to make an API. (1–4) However, their main purpose is to treat the
disease directly by acting upon (via their pharmacological activity) along with
combination of inactive form. Nearly more than 1 lakh tones of pharmaceutical
products are consumed all over the globe (e.g. Europe alone covers up to 24% of
the consumption of medicinal products). Therefore, the generation of these APIs
has stimulated the release of chemicals in the environment and thereby lead to the
spreading of pollution.
 53

Thereby, considering the negative impacts of these chemical channels that are
responsible for generating API, the pharmaceutical companies are rendering
approval to the microbial-based fermentation using bacteria or yeast.

Likewise, the inclination toward microbial-based manufacturing of recombinants

has been increased in the past decade and these manufacturings are liable for the
approvals of FDA for the human use. Adding to the fact, the microbial-based
biopharmaceuticals created the returns of around $100 billion in 2017, and the
business is escalating at a substantial pace (6% CAGR). It is predicted that in the
year 2020 the market demand for fermentation-based protein drugs is expected to
reach $60 billion from $44 billion. Similarly, the demand of peptide hormones and
vaccine, which was $10–19 billion, respectively, is expected to reach $18–28
billion. Today pharmaceutical companies such as Bayer, AbbVie, Biocon,
GlaxoSmithKline, Eli Lilly, Sanofi, and Merck are depending upon microbial
schemes and arrangements for the production of biopharmaceutical products. In
this review, the focused has been laid upon the current and modern developments
that taken place in chemical route of processing of biomass relative to traditional
methods with emphasis on the production of APIs.

These APIs can be natural or synthetic chemical-based active compounds that are
usually found in therapeutic and veterinary drugs. There are chemical-based active
compounds produced using unsafe chemical routes. Therefore, their wide
production, usage, and disposal are getting hazardous to human, water bodies
(including drinking water), and other bio-based lives owing to their uncontrolled
contact to the environment. Furthermore, the presence of these compounds has
been detected in the trace levels from nanograms to micrograms in the last span of
10 years from ground water, drinking water, and waste water. The recent finding
was reported on the pervasiveness of enormous amount of around 18 APIs in the
Lake Victoria-Uganda (in the amount of 5600 ng L −1). Thereby, these APIs have
been established as global contaminants. Although the formation of these chemical
compounds is not from the single source of reaction, rather, they are developed
from many chemical components that are usually initiated from a single
intermediate. Furthermore, several intermediates are formed during the process in
order to convert any raw material into an API. These several reactions usually pass
through the long channels of purification during their developmental engineering,
which involves the usage of huge reactors. Concurrently, these APIs are then
checked for their purity before they are being sold to the drug manufacturers.
 54

In order to generate the chemicals, one of the major biomasses is the

carbohydrates, which constitute about the largest (95%) amongst the organic
compounds of the planet. These are basically exploited for producing further
products either using fermentation or chemical alteration. Biomass in the form of
starch, cellulose, hemicellulose, pectin, and lignin usually exists in the form of
feedstock. In the earlier era of traditional processing starch and other carbohydrate-
rich feedstock were usually being exploited as a raw material by the vivid chemical
industries. Undoubtedly, various products in the form of chemical and polymers
can be generated by using any alteration in the procedure (fermentation) in order to
achieve the desired derivative.

A number of multiple published reports focus on the production of ethanol rather

than other product. Thereby, there are limited number of life cycle assessments
(LCAs) that can generate multiple products. However, from the perspective of
environments as well as economic, most of the bio-based fuels and bioresources
that are produced under the one canopy of the factories are still not a promising
option.

Similarly, forestry-based biorefinery system is one of the specific examples.

Concurrently, there are a number of key factors that have been recognized
considering the environment-favored performance for the generation of bioethanol
and biodiesel. In order to carry out the united production of chemicals, a widened
and well-adapted spectrum is needed. Nevertheless, there are still certain gaps of
reasonable prices that are required for the creation of large-scale biorefineries.
Furthermore, the chemical properties of biomass are not always favorable to
biomass-based raw material; therefore, new technologies are demanding and
challenging amongst the existing companies.

Moreover, the contemporary revolution in the advanced technologies (e.g. genetic

and metabolic engineering, enzymatic engineering) has opened up new avenues for
creating vivid types of industry-based products such as APIs from raw materials
derived from plant. Owing to the preferential use of renewable raw materials of
biomass by the APIs’ chemical industries, the concept of bio refinery has emerged
and can be executed to produce different bio products with the replacement of
chemical-based manufacturing. Renewable resources are good sources as substrate
for the production of green chemicals, APIs, and key starting materials (KSMs),
which come under a vast subject. Therefore, the presented review entirely covers
the major developments and possibilities of lignocellulose as feed stock that
 55

occurred in the recent years in the capacities of renewable biomass as a prominent

foundation of chemicals and their related converted products.

Environmental issues associated with the production of API

chemicals through chemical route

Presently, owing to the considerable increase in the pollution threat to the

environment, more and more API-producing companies have been urged to follow
the greener path in order to reduce the generation of waste (in terms of chemicals,
solvents as by-products) Whereas API-producing companies are always looking
for the faster and economical methods, however, in reality, if we tend to bring
down the generation of waste, then the number of steps for producing API has to
be reduced. Because few and less tangible steps is the primary requisite with
production of solvents or chemicals generated for producing a single pure molecule
of API. Likewise, in addition to cut down the steps, manufactures are further
needed to select nonhazardous types of solvents that possess the ability of
producing proficient and effectual results. Thereby, in order to achieve the results
on greener guidelines, manufacturing companies should employ contract
development officers (CMOs) and further pass their product through the services
of contract development and manufacturing organization (DCMOs) so that the
formulation of the process of API can be planned out at an early stage with the
help of additional screening to avoid unavoidable changes or alteration in the later
stage. This can be accomplished by following the protocols of scale-up processing
in the pilot plants where thorough supervision needs to be administered for
assessing time-to-time assessment and quality control. However, the establishment
of such a kilo lab comes with potential challenges of good manufacturing practices
(GMPs) that require planned budget and diligent supervision. And, by following
these measures, we can reduce the exploitation of raw materials and generation of
by-products.

Concurrently, in the last year’s vivid methods of organic synthesis have been
employed for generating pharmaceutical products, which has strengthened the
medical sector by reducing the causalities, illnesses, and death. However, in order
to achieve this accomplishment, if we are deteriorating the environment
simultaneously then all the efforts of pharmaceutical chemists will go in vain.
Therefore, the pathway of green chemistry is utmost desirable for minimizing the
dreadful impact on the environment. It is widely known that 80% of the wastage in
the form of by-product by the pharmaceutical industry is related to the solvent
 56

reported by GlaxoSmithKline. Thus, the production of the significant amount of

the contaminated solvents will generate the air and other pollutants.

These ways can only be achieved through employing the use of sustainable tools.
These tools call for the nib-to-nib strategy-based research that involves the
following steps in making the processes threat free. The ways of biomass-
generated feedstocks, their bioconversion routes, use of selected harmless
chemicals, and channelized ways of technical processing are the key parameters
that can lessen the environmental issues to the minimal. Similarly, the inline
concept of integrated biorefinery and the continuous use of biosubstrates with the
consumption of nonrenewable sources can safeguard the environment with a
profound relevance. In order to satisfy these parameters, the methodology of LCA
needs to be persuaded that consisted of complete assessment of the products and
processes from start to the end and quantify each environment-based
quantification. Therefore, the only way to drop down the expanding problem is the
generation of green manufacturing practices from pharmaceutical industries with
thorough attentiveness on the selection, use, recovery, and disposal of the
chemicals.

3.Method of biomasses conversion in APIs synthesis

Presently, the environmental amicably processes are becoming tremendously

popular for the conversion of biomass to APIs. As following this route, we can be
able to bring reduction in the rate of global warming. There are multiple processes
that can convert lignocellulosic biomass to APIs in terms of fermentation to form
pharmaceutical ingredients.

3.1. Chemical approach

The processes that transform the biomass to value-added chemicals (furfural,

levulinic acid, etc.) in the presence of catalyst (hydrosulfuric, hydrochloric, and
phosphoric acids) and conditions of high temperature and pressure fall under
chemical conversions. Although the factors of low yield are always being
confronted as major challenges for commercialization. Therefore, in order to
bridge the gap between the challenges, various innovative methods have been
employed to convert biomass to chemicals. Likewise, a novel process was reported
using catalysts based on modified carbon that were expanded to transform organic
acids and sugar by the Northwest National Laboratory.
 57

Furthermore, the performance of zeolites has been exploited for the conversion of
biomass to APIs, and it was observed that the usage of zeolites was found to be
remarkable owing to their selective size and shapes and they have been proved as
potential catalysts. In addition, the strength and constancy of silica-based catalysts
were reported for converting glucose to sorbitol. The research was carried not only
in the field of innovated catalysts but also for the innovative pathways, and the
routes were also investigated for the selective conversion of important chemical
(e.g. production of hydroxymethyl furfural). Concurrently, the formation of acetic
acid from biomass using supercritical water employing hydrothermal processing
was also reported. Moreover, there are certain chemical intermediates (3-
hydroxypropionic acid) that also formed and foster the formation of final stage
products as tetra-hydro furan (THF) and gamma-butyrolactone from 1, 4-diacids,
and 1,3-propanediol.

There are certain monosaccharides like glucose and xylose that can be converted to
different chemicals through the process of bioconversion following the route of
chemical processing. Thus, glucose is an essential and foundational raw material
for the bioindustry as crude oil is to the petrochemical industry. Sources of starch
like corn, tapioca, wheat, and potato are profoundly known to produce glucose
using enzymatic hydrolysis on an industrial scale. According to the report by Kim
and Dale, 3.5 million tons (MT) of lactic acid produced (10 times higher than the
current annual lactic acid production) from using hydrolysis of approximately 1500
MT of crop residues and approximately 73.9 MT of fruits residues were obtained
from rice, maize, barley, sorghum, and sugar cane.
3.2. Biotechnological approaches

The pathway of biotechnological approaches explored the usage of biocatalyst

(enzymes) or cells for the transformation of biomass into utility chemicals. In
nutshell, it is considered as one of the most easy, simple, and convenient methods
for the formation of industrial products from biomass. In contrast to chemical
conversions that involve high temperatures and pressures, biological conversions
are relatively mild. However, the concept of these biotechnological-based
conversions is not the novel addition because earlier as well the various
commercially used chemicals are being produced from yeast and bacteria (in terms
of acetone-butanol, citric acid ethanol, lactic acid, etc.). The merits of less
formation time of by-products and higher yield of product and selectivity (of
biocatalysts) to convert renewable resources into chemicals have created
fascination in recent time.
 58

Although there are certain limitations in the processing of fermentation owing to

various variations in the pathway of microorganisms, we cannot produce large
variety of products. Concurrently, there is a strong demand of novel processing
techniques in order to widen the scale of products. Therefore, the only way to bring
variety and resolve the limitations of biotechnological pathways is to involve the
technologies based on genetic engineering and recombinant DNA technology,
which can alter the gene coding and can bring about the desired changes for the
sugar metabolism. Likewise, modified Escherichia coli proved useful for the
production of the compounds (catechol and adipic acid) from glucose.
Recombinant Saccharomyces yeast converts glucose and xylose present in
cellulosic biomass into ethanol.

Moreover, there is production of chemicals obtained from biomass using

immobilized enzyme and whole cells. Huang and Yang used rotating fibrous
matrix of immobilized Rhizopus oryzae cells to produce fumaric acid from glucose
and corn starch. Conversion of biomass hydrolyzate into chemical by absorbing it
on solid metal oxide support using microbial process with compounds produced
from lignin and fermentation inhibitors to enhance yield has been patented by
Hames et al.

That is why persistent efforts have been made for the alteration of enzymes and
living organisms to produce the desired chemicals and particularly from the
renewable sources. High yield and selectivity as well as minimal waste streams
favor biological conversions as pathways for converting biomass into higher value
chemicals. But there are numerous hindrances with the ongoing biological-based
transformations (e.g. the higher energy requirements, lower production rates,
continuous stirring) for achieving the desired results in bulk.

Biorefineries are largely required during the fermentation process of saccharides

for their transformation to chemical-based by-products. Thereby, this process
fostered the raw materials to their complete degradation to unalloyed sugar
solutions and generic feedstocks. Microorganisms are then used in fermentative
medium to produce metabolic product in excess. Thereby, these metabolic
products can further be utilized for the conversion of huge chemicals employing
the biological or chemical route. However, the essential 12 molecules reported as
the most favorable for the utilization in the conversion of biomass are arabinitol,
aspartic acid, fumaric acid, malic acid, glutamic acid, glycerol, levulinic acid,
malic acid, succinic acid, sorbitol 2,5- furandicarboxylic acid, 3-
hydroxybutyrolactone, and 3-hydroxy-propionic acid. A glucose-based media was
 59

proposed for the production of 3-hydroxypropionic acid and above mentioned

chemicals using fermentation could be enhanced by using genetically engineered
microorganisms and stated that from the chemical conversion of saccharides that
obtained from biomass molecules namely glucaric acid, levulinic acid, 2,5-
furandicarboxylic acid, 3- hydroxybutyrolactone.

3.3. Metabolic approach for API production

The branch of metabolic engineering is one of the empowering skill of science that
has an eminent role in the expansion and progress of cell factories to further
produce pharmaceuticals, fuels, chemicals, and food ingredients via following the
route of microbial fermentations. With the burgeoning and opening outgrowth of
genetic engineering, it probably became much realistic to generate the miniature
protein-based compounds like insulin, certain growth hormones employing the
process of fermentation. Concurrently, metabolic engineering created the pathway
for converting the minute microbes into cellular factories, owing to inexpensive
raw materials like biomass-derived sugars to fuels and chemicals. In the reported
literature by Hong et al., various industry uses of novel bioprocesses were shown
for converting feedstock to agricultural-based products. One of its different biotech
pathways was recently explored by DSM (Dutch multinational corporation) for the
production of antibiotic cephalexin, which was earlier followed for the chemical
conversion of penicillin. Similarly, Novozymes has formed a clubbed endeavor
with Cargill with the interest of developing a bio-based procedure for the
manufacturing of 3-hydroxypropionic acid. Nevertheless, Gevo has further created
the opportunity of biofuel by following a process for the production of isobutanol.
In addition, Amyris has further developed a yeast-based fermentation process for
the production of farnese that can be employed as biodiesel and can also be
converted into squalene, which has wide usage in cosmetics.

It was seen that CA is produced through the submerged strains of Streptomyces

clavuligerus. Thereby, in order to increase the production, several wide strains
have been explored by Ser et al.. The most commonly available carbon source, i.e.
glycerol, has also been employed in cultivating S. clavuligerus to produce CA,
which was found to hike the cultivation up to fivefold . Amongst the latest
findings, the role of yeast Saccharomyces cerevisiae was also found as a major cell
factory for producing vivid industrial products. Similarly, our group is also
working on this yeast for the production of butanol in order to use it further for the
multiple applications in pharmaceutical industry and biofuels (e.g. biodiesel).
 60

A multiple number of hypothetical studies have explained the utility of cell factory
for producing a wide range of chemicals, viz., lactic acid, glycerol, and malic acid.
Moreover, the multiplicity of isoprenoids is further getting huge and thereby
indicating the creation of other bioactive compounds through the medium of novel
enzymes that can be explored for chimeric pathways. For these reasons, there has
been wide attentiveness in mounting microbial-related production of isoprenoids
through following plant-based pathway with some significant genetic
modifications of leader sequence and for relocating the relative genes.

4. Some important types of API chemicals

4.1. Shikimic acid

In the pharmaceutical industry, shikimic acid is extensively used for the synthesis
of chiral buildings block. Shikimic acid-based antiviral drug oseltamivir is used in
the treatment as well as prophylaxis for the patients suffering from influenza (A,
B). Shikimic acid also plays a key role in the development of an anti-influenza
medicine termed as Tamiflu . But the production of an increased amount of
Tamiflu falls under the hazardous category. Owing to the existence of the
conditions of mild reaction, careful handling is required as chemistry of potentially
explosive is involved in the synthesis steps of this drug reaction. To bring down the
uptake of shikimic acid by E. coli capable of synthesizing shikimic acid, methyl-α-
D-glucopyranoside that mimic glucose was added to the culture medium as it is
anticipated that transport systems of shikimic acid are controlled by catabolite
repression. Minimization of formation of quinic acid (0.09 to 0.01 mol/L)
considerably throughout due to the incorporation of methyl-α-D-glucopyranoside
as a substitute to glucose. The yield initially rose from 0.14 to 0.19 mol/L based on
glucose and the yield of shikimic acid from 28 to 35 g/L due to the addition of
methyl-D-glucopyranoside. Aromatic amino acids and aromatic vitamin can be
assessed using shikimic acid with the help of strains of E. coli that blocked the first
three steps of the Pittard and Wallace aromatic amino acid pathway. Currently, the
use of fermentative approaches on E. coli by Swiss pharmaceutical company
named Roche produces shikimic acid. However, the major concern is the
production of large number of bioproducts produced during the synthesis of
shikimic acid. It has been reported by various researchers that if we limit the
carbon source during fermentation of shikimic acid large amount of bioproducts
are formed. However, if the medium is replenished with high carbon source it leads
to accumulation of high shikimic acid. It has been found that phosphate-limiting,
carbon-rich growth conditions support shikimate production over by-products, and
 61

limiting carbon growth induces the formation of by-products. This involves the
blockage of aromatic amino acid pathway post shikimiate-3-phosphate (S3P)
production. S3P was converted into shikimic acid owing to the activity of bacterial
phosphatases. Draths et al. found that in rationally engineered E. coli strains the
production of shikimic acid by metabolic engineering is the most advanced after
the amino acid pathway in these strains and the disruption of the K and L genes
(that are responsible for encoding shikimate kinase I and II) was blocked.
Furthermore, dairy effluent (whey) may be a good source of glucose extract from
enzymatic hydrolysis of whey. This glucose may be use as substrate for the
production of shikimic acid (Figure 1)

Systematic representation of utilization of dairy waste (whey) for the production of

APIs.
4.2. Succinic acid

Succinic acid or butanedioic acid (C4H6O4) or amber acid is a common metabolite

in plants, animals, and microorganisms and is further found in beer, coal, meat,
eggs, honey peat, molasses, fruits, and urine. First purified from ‘amber’, the old
fossilized resin of ancient trees, conifers in 1546, and has established wide
applications till now. It has been known for curing alcohol hangovers by
processing acetaldehyde, which is the most toxic metabolite of alcohol. Succinates
are generally used for medicinal purposes as sedatives, antispasmers, antirheoters,
contraceptives, inhibitor of potassium ions, and antioxidants.
 62

The linear saturated structure of succinic acid has been acknowledged as the
potential intermediate for the synthesis of industry-related chemicals of great
relevance. Succinic acid has wide applications ranging from radiation dosimetry to
agriculture, food, medicine, plastics, cosmetics, textiles, plating, photography, and
waste gas scrubbing. It serves as feedstock for the manufacture of many
commodity chemicals like polybutyrate succinate (PBS) and polyamides through
esterification reactions. Showa Highpolymer Co., Ltd., Tokyo, Japan, has been
known to manufacture ‘Bionelle,’ a biodegradable plastic that is succinic acid and
1,4-butanediol ester that is the newest application of succinic acid.

This is relatively due to the price of chemicals capable of forming succinic acid
from maleic anhydride, which has greatly reduced its industrial applications.
Moreover, succinic acid is produced commercially through chemical synthesis by
hydrolysis of petroleum products, lignocellulosic biomass (Figure 2), and also
creates environmental issues. Currently, green technology has become a driving
force in the chemical industry in order to control pollution produced by processing
of petrochemical and solves the issues for supply by basing production of
hydrocarbons on a renewable environmental-friendly carbohydrates economy.

Systematic representation for the production of succinic acid using lignocelluosic

biomass.
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4.3. Erythritol

It is a sugar-based alcohol that has been regarded as a low-calorie sweetener all

over the globe. Erythritol naturally occurs in various fruits and fermented foods. It
is usually generated from glucose with the process of fermentation
(using Moniliella pollinis, yeast) and food-grade osmophilic yeast ferments the
glucose that can be used for the production of erythritol. It is nearly (of about 60–
70%) a non-caloric sugar that at the same time neither alters the levels of blood
suga, nor causes tooth decay. Food-grade osmophilic yeast ferments the glucose
that can be used for the production of erythritol. Erythritol is purified after
removed from the fermentative broth, and 99% purity was found in the final
crystalline product. It does not pose any side effect of gastric-related problems
owing to its distinctive metabolism of digestion. Due to the occurrence of erythritol
in foods, the US per capita, the consumption of erythritol is estimated to be 80
mg/person/day. It has been confirmed that body fluids of humans and animals
contain erythritol. It has levels of approximately 1.2 mg/L in human plasma as well
as fetal blood of animals. Human urine has 10–100 mg/L concentrations of
erythritol. However, renowned countries as Japan and the United States have
already marked it as zero-calorie sugar, wherea, European regulations currently
label it under nearly low calorie sugar (~0.24 kcal/g).

Challenges and solutions to overcome the production of APIs

chemicals through biotechnological route

This review emphasized numerous problems that are being confronted by big
companies to industrialize the chemical and fuel synthesis technology (biomass
collection and transport, biomass pretreatment, characterizations of treated
biomass, fermentation, and chemical separation). Biomass location, terrain, type of
residue, way into the field, and accessibility of machines are some of the aspects
that influence the selection method for collection and harvesting of biomass.
Biomass is collected using equipment and tractors with the help of labor. Baling
choices include twine, plastic wrap, and net wrap. Source of biomass greatly
determines the cost, e.g. biomass from forest residue and straw residue from
cultivable land and small farms waste have different costs. After harvesting,
distinctive methods are applied for biomass pretreatment. Supply of biomass to the
industries plants can be either in trucks, ships, and trains based on the transport
distance. Transportation of biomass using ships to a harbor is further unloaded and
allocated by trucks for short distance and trains for long distances. Large
 64

companies that have investment to introduce a new biomass-based biorefinery are

currently irritating to bring different new (and lineup) process methodologies that
still have numerous compound separation and compound purification challenges to
resolve. These include drying, chopping, grinding, shredding, pelletization,
carbonization, and torrefaction. The process of torrefaction is a thermochemical
process that comprises 50°C/min low heating rate, 200°C and 300°C of
temperature range in the absence of oxygen. Another method widely used for
decomposing biomass in the absence of oxygen is slow pyrolysis with temperature
range between 400°C and 800°C and fast pyrolysis having temperature range
between 450 and 550°C.

Characterization of biomass consists of particle size and shape characterization

using mechanical sieving and laser diffraction. For flow and feeding properties of
biomass angle of repose test (AoR), compressibility tests and shear cell tests are
used. Other properties, namely, grindability, density, flowability, and energy
content, have been estimated by hardgrove grindability Index, particle density,
flow index, and oxygen bomb calorimeter method, respectively. Near-infrared
(NIR) spectroscopy, which is a nondestructive approach, relies on specific bond
detection and quantitation. Concurrently, the logistics of biomass and techno-
economic assessments are employed to evaluate the technology readiness level
(TRL). Then assessments of the environmental impacts of the use of various
technologies are created. Once suitable biomass feedstock, biomass pretreatment
techniques, and enzymes are joined to synthesize inexpensive sugars, and then the
selection of fuels and chemicals depends on the commercial market and can more
significantly be derived from the biofuel strategy (implemented by the native and
federal government). Additionally, in order to race with the price of fossil fuel, the
price of biorefinery handling should be retained as less as possible by energy
effective techniques and by the use of less amount of water. Consequently, it is
highly significant to take the full advantage of the difference in energy expended
and synthesized. Otherwise, the successfulness of a biorefinery concept will be
assessed by the gross energy that is synthesized using the various processing steps.

In addition to energy, one of the major challenges that come across is the
availability of the substrate. The continuous supply of substrate is the primary
prerequisite for keeping the uninterrupted production of the required ingredients.
Further, the processes of recovery and purification (downstream processes)
involved decide the destiny of the molecules formed from the biomass. Moreover,
the fate of fermentations costs, production costs, operation costs, etc., is one of the
frontline challenges of this stream. Concurrently, the less tangible the downstream
 65

processes the more will be the yield. The overcoming of these bottlenecks is also
the most technical requirement for potent generating pharmaceutical ingredients
from the huge masses of biomass. Consequently, these challenges are highly
significant for the processing of biomass wastes. Therefore, by converting the
above challenges into strategies, the conversion of biomass to useful ingredients
can be achieved efficaciously.

Future prospect of biomass to active pharmaceutical ingredient

chemicals

To recycle the biomass and conversion of valuable bioproducts, streamline

approaches are needed to continuous identify the novel technologies. However,
utilization of biomass and conversion by the Active Pharmaceutical Ingredients
Committee (APIC) in the circular bioeconomy noticed various challenges in terms
of fulfilling the consumer demand and business opportunities. In addition, the
exploitation of biomass and conversion of APC with circular bioeconomy has great
advantages but still needs to put emphasis on proper handling of biomass and strict
policy for waste recycling and management.

Recent biotechnology approaches like genetic engineering and bioengineering help

to develop novel microbial strain or its consortium as well as advance model that
mainly focused on improved various aspects like enhanced production of biomass
yield, CO2 utilization, lipid accumulation, and bioremediation ability. Thus,
integration of various technologies and computer engineering approaches will play
a vital role on the way forward to achieve circular bioeconomy biomass-based
valuable bioproducts like APC and biofuels. However, looking at present scenarios
more questions have been raised than answers for the efficient utilization of
biomass because it results in huge quantity of biomass like agricultural waste and it
was burned either due to lack of knowledge or availability modern equipment. In
addition, due to overexploitation of nonrenewable energy resources along with its
high-cost chemicals it has forced the industries to identify sustainable, cost-
effective, and renewal energy resources to look for long-term solutions for
recycling of organic biomass. Thus, recycling of biomass and its conversion to
APC is a significant approach for utilization of organic waste and
biotransformation of valuable end products.

Although several approaches are used to learn biomass to resource and its
conversion in APC, a critical overview of the technologies used till date is limited
 66

and is not abundantly available. Hence, extensive research with molecular and
biochemical tools is required to elucidate the remediation mechanism and focus on
cost-effective and sustainable commercial exploitations. In addition, the
combination of omics resources facilitates the production of more metabolites and
bioactive compounds of interest that will ultimately lead to accelerating the drug
discovery.

Conclusion

A huge quantity of biomass is getting collected either in the form of agricultural

process or food processing/manufacture. Instant disposing of them without any
treatment creates environmental threat, thereby more sustainable technologies are
an attractive option to efficiently recycle it because its available in low cost and
can be converted to multiproducts. In this review article, various economically
viable technologies have been discussed comprehensively for biochemical
conversion of agriculture biomass into valuable APC such as pharmaceuticals,
biopolymers, bio-solar cells, fine chemicals, lubricants, etc. Advances in the
technologies can generate bio-based economy and at the same time reduce the
associated environmental risk. In addition, more future studies are the mandatory
prerequisites in order to combine various technologies and restrict the
secondary/tertiary pollution level to an efficient way through the channelized
utilization of bioresources and to result in profitable business.
 67

Drug Designing

Drug design is the process of discovering and developing new pharmaceutical

compounds, often referred to as "drug discovery." It involves a combination of
scientific disciplines such as chemistry, biology, pharmacology, and computational
sciences. Drug design involves the design of molecules that are complementary in
shape and charge to the molecular target with which they interact and bind. Drug
design frequently but not necessarily relies on computer modeling techniques and
bioinformatics approaches in the big data era.

Here's a high-level overview of the key steps and concepts in drug design:
1. Target Identification
- The first step is identifying a biological target, typically a protein or nucleic acid,
implicated in a disease. This target could be an enzyme, receptor, or another
molecule involved in a disease process.
 68

2. Target Validation
- After identifying a target, researchers need to validate that it plays a critical role
in the disease. This involves experimental studies to confirm that modulating the
target can affect the disease's outcome.

3. Lead Compound Identification

- Once the target is validated, the next step is to identify compounds that can
interact with the target. This often involves high-throughput screening, where
thousands or millions of small molecules are tested against the target to find
those with potential therapeutic effects.

4. Lead Optimization
- After finding a lead compound, researchers optimize its structure to improve
properties like potency, selectivity, pharmacokinetics (how the body absorbs,
distributes, metabolizes, and excretes the drug), and safety.

5. Structure-Based Drug Design

- This approach uses the three-dimensional structure of the target to guide the
design of new compounds. Techniques like X-ray crystallography and nuclear
magnetic resonance (NMR) spectroscopy help determine the target's structure,
and computational tools are used to model interactions with potential drugs.

6. Preclinical Testing
- Optimized lead compounds undergo preclinical testing in cell-based assays and
animal models to assess efficacy, safety, and toxicity. This step helps identify
any potential adverse effects and further refine the compound's properties.
 69

7. Clinical Trials
- If a drug candidate shows promise in preclinical testing, it moves to clinical
trials. Clinical trials involve multiple phases:
Phase I Tests safety and dosage in a small group of healthy volunteers.
Phase II Evaluates efficacy and side effects in a larger group of patients with the
target disease.
Phase III Involves large-scale testing to confirm efficacy and monitor adverse
reactions.

8. Regulatory Approval
- After successful clinical trials, the drug developer submits an application to
regulatory agencies like the U.S. Food and Drug Administration (FDA) or the
European Medicines Agency (EMA) for approval. This involves detailed
documentation of the drug's development, clinical trial results, and
manufacturing processes.

9. Post-Marketing Surveillance
- Even after approval, drugs undergo continuous monitoring for safety and
efficacy in real-world use. This is known as pharmacovigilance and helps detect
any long-term or rare adverse effects.

10. Drug Patents and Commercialization

- Patents protect drug developers' intellectual property, giving them exclusive
rights to market the drug for a certain period. Once the patent expires, generic
versions of the drug can be produced.
 70

Drug design is a complex, iterative process that can take years or even decades from
discovery to market. It requires collaboration among scientists, clinicians, and
regulatory bodies to ensure that new drugs are safe, effective, and meet patients'
needs.
 71

Softwares in Chemistry

Chemistry software encompasses a wide range of tools used for research, teaching,
and industrial applications. These programs help scientists analyze chemical data,
model chemical structures and reactions, visualize molecular systems, and much
more.
Chemdraw

ChemDraw is a popular software program used by chemists and researchers for

drawing chemical structures, reactions, and diagrams. Developed by PerkinElmer,
It provides a user-friendly interface and a wide range of tools and features tailored
to the needs of chemical professionals. Here's an overview of what ChemDraw
offers:
1. Chemical Structure Drawing: ChemDraw allows users to draw chemical
structures with ease, including organic molecules, inorganic compounds, polymers,
and biochemical substances. It provides a comprehensive set of tools for creating
bonds, atoms, rings, and other structural elements.
2. Reaction Drawing: ChemDraw enables users to depict chemical reactions,
including mechanisms, arrows, and stoichiometry. It supports various types of
reactions, such as addition, elimination, substitution, and redox reactions.
3. Spectral Analysis: ChemDraw includes tools for analyzing and annotating
spectroscopic data, such as NMR spectra, IR spectra, and mass spectra. Users can
 72

label peaks, integrate areas, and generate spectral assignments directly within the
software.
4. 3D Structure Visualization: ChemDraw allows users to view and manipulate
three-dimensional molecular structures, enabling them to visualize molecular
conformations, stereochemistry, and spatial arrangements.
5. Database Integration: ChemDraw seamlessly integrates with chemical
databases and libraries, allowing users to access a vast collection of chemical
compounds, reactions, and properties. It supports popular databases like SciFinder,
Reaxys, and ChemSpider.
6. Publication-Quality Graphics: ChemDraw produces high-quality graphical
representations suitable for publication in scientific journals, presentations, and
reports. It offers customizable styles, templates, and export options to meet the
formatting requirements of various publications.
7. Collaboration and Sharing: ChemDraw facilitates collaboration among
researchers by enabling the sharing and exchange of chemical structures and data.
Users can export files in standard formats like MDL Molfile, ChemDraw CDX,
and SMILES for compatibility with other software programs and platforms.
8. ChemOffice Suite Integration: ChemDraw is part of the ChemOffice Suite,
which includes additional tools for chemical informatics, data analysis, and
modeling. Users can seamlessly transition between different applications within
the suite for comprehensive chemical research workflows.
Overall, ChemDraw is an indispensable tool for chemists and researchers engaged
in molecular design, analysis, and communication. Its intuitive interface, extensive
feature set, and integration capabilities make it a valuable asset in both academic
and industrial settings.
 73

Zotero

Zotero is a versatile reference management tool that can be incredibly useful for
researchers in the field of chemistry. Here's how Zotero can specifically benefit
chemists:
1. Organization of Research Papers: Zotero helps chemists organize their
research papers, articles, patents, and other scholarly materials in a systematic
manner. With features like folders, tags, and collections, researchers can categorize
their references based on topics, projects, or publication types.
2. Citation Management: Zotero streamlines the process of citing sources in
research papers, lab reports, and other academic documents. Chemists can easily
insert citations in various citation styles (such as ACS, APA, or MLA) directly
from their Zotero library into their manuscripts. Zotero automatically generates
bibliographies, ensuring accurate and consistent citation formatting.
3. Collection of Chemical Information: Chemists often need to collect information
on chemical compounds, reactions, and properties from various sources such as
journals, databases, and websites. Zotero allows users to save references with
metadata, including titles, authors, abstracts, and keywords. This makes it easy
for chemists to retrieve and reference relevant information during their research.
 74

4. Management of Laboratory Protocols: In addition to academic papers, Zotero

can also be used to organize laboratory protocols, experimental procedures, and
technical manuals. Chemists can create separate collections for different types of
protocols and annotate them with notes or comments for future reference.
5. Collaboration with Peers: Zotero facilitates collaboration among chemists
working on collaborative research projects or publications. Researchers can share
their Zotero libraries with colleagues, collaborators, or students, enabling them to
access and contribute to a shared pool of references. Comments and annotations
can be added to shared references, fostering communication and collaboration.
6. Integration with Chemistry Databases: Zotero integrates seamlessly with
popular chemistry databases and search engines, such as SciFinder, Reaxys, and
PubMed. Chemists can import references directly from these platforms into their
Zotero libraries, saving time and effort in building their reference collections.
7. PDF Management and Annotation: Zotero allows chemists to attach PDF files
to their references and annotate them directly within the software. Researchers
can highlight important sections, add comments, and extract text or images from
PDFs for further analysis.
8. Cross-Platform Access: Zotero offers cloud synchronization, enabling chemists
to access their reference libraries from multiple devices, including computers,
tablets, and smartphones. Changes made to references or annotations are
automatically synced across all devices, ensuring seamless access to up-to-date
research materials.
Overall, Zotero is a valuable tool for chemists, providing a centralized platform for
managing, organizing, and citing research literature and laboratory information. Its
user-friendly interface, robust features, and integration capabilities make it an
essential asset for researchers in the field of chemistry.
 75

ImageJ

ImageJ is a powerful open-source image processing and analysis software that is

widely used across various scientific disciplines, including chemistry. Here's how
ImageJ software can be utilized in chemistry:
1. Image Analysis of Chemical Structures: ImageJ can be used to analyze
images of chemical structures, such as crystallographic data or microscopy images
of molecular assemblies. Researchers can quantify parameters like particle size,
shape, distribution, and density using ImageJ's built-in analysis tools.
2. Spectral Analysis: ImageJ supports the analysis of spectral data obtained from
techniques like UV-Vis spectroscopy, fluorescence spectroscopy, and Raman
spectroscopy. Researchers can import spectral images or spectra and perform
spectral processing, such as peak identification, integration, and quantification.
3. Quantification of Chemical Reactions: ImageJ can be used to analyze images
of chemical reactions, such as chromatograms from gas chromatography (GC) or
 76

thin-layer chromatography (TLC). Researchers can quantify peak areas, retention

times, and concentration gradients using ImageJ's image analysis algorithms.
4. Quantitative Microscopy: ImageJ is widely used in quantitative microscopy
studies in chemistry. Researchers can analyze images of cells, nanoparticles, or
biomolecules to measure parameters like cell size, fluorescence intensity,
colocalization, and particle tracking.
5. Crystallography and Crystallographic Image Processing: ImageJ can assist
in crystallographic image processing tasks, including indexing, integration, and
data reduction of X-ray diffraction images. Researchers can use ImageJ plugins or
macros to automate crystallographic data analysis workflows.
6. Visualization and Image Enhancement: ImageJ provides tools for visualizing
and enhancing chemical images, such as adjusting brightness, contrast, and color
balance. Researchers can generate publication-quality images and figures for
scientific publications and presentations.
7. Customization and Plugin Development: ImageJ is highly customizable,
allowing researchers to develop custom image analysis algorithms and plugins
tailored to specific chemistry applications. Researchers can extend ImageJ's
functionality by writing scripts in languages like Java, Python, or JavaScript.
8. Integration with Other Software: ImageJ can be integrated with other
software tools commonly used in chemistry, such as ChemDraw for chemical
structure drawing or MATLAB for advanced data analysis. Researchers can import
and export data between ImageJ and other software platforms seamlessly.
Overall, ImageJ is a versatile and flexible software tool that can be applied
to a wide range of tasks in chemistry, from analyzing chemical structures and
spectra to quantifying chemical reactions and processing microscopy images. Its
open-source nature, extensive plugin ecosystem, and user-friendly interface make
it a valuable asset for researchers in the field of chemistry.
 77

OriginPro

OriginPro is a powerful scientific graphing and data analysis software widely used
in various scientific disciplines, including chemistry. Here's how OriginPro can be
utilized specifically in chemistry:

1. Data Visualization: OriginPro allows chemists to create publication-quality

graphs and plots to visualize experimental data. Whether it's plotting titration
curves, chromatograms, or spectroscopic data, OriginPro offers a wide range of
customizable graph types and options to effectively communicate research
findings.
2. Data Analysis: OriginPro provides advanced data analysis tools tailored to the
needs of chemists. Researchers can perform statistical analyses, curve fitting, peak
analysis, and baseline correction to extract meaningful insights from experimental
data. OriginPro's intuitive interface and extensive analysis capabilities make it an
invaluable tool for analyzing chemical data sets.
3. Spectral Analysis: OriginPro supports spectral analysis techniques commonly
used in chemistry, such as UV-Vis spectroscopy, infrared spectroscopy (IR), and
nuclear magnetic resonance (NMR) spectroscopy. Chemists can import spectral
data files, perform spectral processing, and analyze peak positions, intensities, and
shapes to characterize chemical compounds and reactions.
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4. Kinetic Analysis: OriginPro facilitates kinetic analysis of chemical reactions by

providing tools for modeling reaction kinetics, calculating rate constants, and
fitting kinetic models to experimental data. Chemists can analyze reaction progress
curves, determine reaction orders, and assess reaction mechanisms using
OriginPro's kinetic analysis features.
5. Surface and 3D Plotting: OriginPro enables chemists to visualize three-
dimensional surfaces and contour plots of chemical data, such as molecular orbital
surfaces, reaction energy landscapes, and electrochemical potential maps.
Researchers can manipulate and analyze 3D plots to gain insights into molecular
structures and interactions.
6. Chemometrics and Multivariate Analysis: OriginPro supports chemometric
analysis techniques, such as principal component analysis (PCA), partial least
squares (PLS), and cluster analysis. Chemists can use OriginPro to explore
relationships between multiple variables in complex chemical data sets and extract
relevant information for classification, prediction, and pattern recognition.
7. Customization and Automation: OriginPro offers extensive customization
options and automation capabilities to streamline data analysis workflows in
chemistry. Researchers can create custom templates, scripts, and batch processing
routines to automate repetitive tasks and enhance productivity.
8. Integration with Other Software: OriginPro can be integrated with other
software tools commonly used in chemistry, such as MATLAB, Python, and
ChemDraw. Researchers can import and export data between OriginPro and other
software platforms seamlessly, enabling interoperability and data exchange.
Overall, OriginPro is a versatile and comprehensive software tool that
empowers chemists to analyze, visualize, and interpret chemical data effectively.
Its robust features, user-friendly interface, and extensive analysis capabilities make
it an indispensable asset for researchers in the field of chemistry.
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Conclusion
The On-the-Job Training (OJT) program in chemistry offers a comprehensive and
dynamic learning experience that equips participants with essential skills and
knowledge to excel in the field. Throughout this program, we have had the
opportunity to delve into various aspects of chemistry, ranging from basic
techniques to specialized areas such as UV and IR spectroscopy, gas
chromatography, and drug designing.
By mastering basic techniques such as measurement, mixing, and titration, we
have developed a solid foundation for conducting experiments safely and
effectively. We have also gained proficiency in utilizing a wide range of laboratory
equipment, including balances, glassware, and chromatography systems, enabling
them to perform experiments with precision and accuracy.
Furthermore, we have explored advanced techniques such as UV and IR
spectroscopy, which are instrumental in analyzing the molecular structure of
compounds. Through hands-on experience with spectrophotometers, we have
learned how to interpret spectral data and draw meaningful conclusions about
chemical substances.
The training program has also provided insights into the pharmaceutical industry,
including the development and manufacturing of Active Pharmaceutical
Ingredients (API). We have gained an understanding of the regulatory landscape
and intellectual property rights associated with pharmaceutical innovations,
preparing them for potential careers in this highly regulated sector.
Moreover, we have been introduced to the fascinating field of drug designing,
utilizing software applications and molecular modeling techniques to facilitate
rational drug discovery. This exposure to cutting-edge technologies and
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methodologies has broadened their horizons and inspired us to explore innovative

solutions to real-world challenges in chemistry and pharmacology.
Overall, the OJT program in chemistry has empowered us to become proficient and
confident professionals, ready to make meaningful contributions to the field. As we
embark on our career journeys, we will carry with us not only technical skills but
also a passion for discovery, innovation, and lifelong learning. We are confident
that they will continue to thrive and excel in their chosen paths, shaping the future
of chemistry and pharmaceutical sciences for years to come.