SPECTROSCOPY AND COMPUTATIONAL

CHEMISTRY

Unit-5
UNIT-5 SPECTROSCOPY AND COMPUTATIONAL CHEMISTRY

Spectroscopy – introduction and EMR-Matter interaction. Beer-Lambert’s law (no

derivation). UV-Visible spectroscopy - instrumentation (block diagram) and

applications. IR spectroscopy - instrumentation (block diagram) and applications.

Computational chemistry - molecular dynamics and chemical reactivity, Quantum

mechanical methods – DFT basics for chemical reactivity. Softwares and Applications

of Cheminformatics, Basic Principles and Block Diagram for IoT and Green IoT –

Applications of IoT in biomedical applications, Artificial intelligence - machine

learning and deep learning methods to predict physicochemical properties.

SPECTROSCOPY

✓ Spectroscopy is the branch of science dealing with the study of interaction

of electromagnetic radiation with matter.

✓ It is a powerful tool available for the study of atomic and molecular

structure and it is also used in the analysis of most of the samples..

The study of spectroscopy is divided into two types.

1. Atomic spectroscopy:

2. Molecular spectroscopy.
Electromangnetic radiation (or) Electromagnetic energy (or)
Radiant energy

❖ Electromagnetic radiation is produced due to the interaction

between the electric field and the magnetic field.

❖ Electromagnetic radiation is an oscillating electric and magnetic

disturbance that spreads as a wave through empty space, the
vacuum.

❖ Electromagnetic radiation is divided into number of regions

according to their wave length.

❖ It can be represented as, λ (lambda)

Characteristics of Electromagnetic Radiations (Or) Waves and their Characteristics:
 Electromagnetic Radiation

❑ Amplitude: Amplitude is the distance from the maximum vertical displacement

of the wave to the middle of the wave.

❑ Wave length(λ): It is the distance between two crests or troughs.

❑ Frequency(υ): It is defined as the number of waves which can pass through a

point in one second.
❑ Wave Number(ΰ): It is the reciprocal of wave length and is defined as the total
number of waves which can pass through a space of 1cm.
 Electromagnetic spectrum (EMS)

The arrangement of all types of electromagnetic radiations in the increasing order of

their wavelength or decreasing order of their frequency is known as Electromagnetic
Spectrum.
Types of Spectroscopy
Spectroscopy UV-Vis Spectra

Infra Red spectra

 UV-Visible Spectroscopy
Principle
❖ Visible and Ultraviolet (UV) spectra arises from the transition of valency electrons
within a molecule or ion from a lower electronic energy level (ground state E0) to
higher electronic energy level (excited state E1).
❖ This transition occurs due to the absorption of UV (wavelength 100-400 nm) or
visible (wave length 400-750 nm) region of the electronic spectrum by a molecule
(or) ion.
❖ The actual amount of energy required depends on the difference in energy between
the ground state and the excited state of the electrons.
E1 − Eo = hν.
 Energy level diagram (or) Electronic transitions

Energy absorbed in the visible and UV region by a molecule causes transitions of valence
electrons in the molecule.
These transitions are σ → σ∗, n → σ∗, n → π∗ and π → π∗.
The energy values for different transitions are in the following order. Where,

n → π∗< π → π∗< n → σ∗<< σ → σ∗

Energy level diagram

 UV-Visible Spectroscopy
Some important terms:
Chromophores:
The presence of one or more unsaturated linkages (π) in a electrons is responsible for
the colour of compound, these linkages are called chromophores. Example: C=C, C=O,
N=N, Alkyne
Auxochromes:
It refers to an atom or groups which does not give rise to absorption band on its own,
but when conjugate to chromophore will cause a red shift. Example: -OH, -NH2, -Cl, -I
Some other terms:
Bathochromic Shift (Red shift): Shift to higher wavelength.
Hypsochromic shift (Blue Shift):Shift to lower wavelength
Hyperchromic effect: An increasing intensity
Hypochromic effect: A decrease in intensity
INSTRUMENTATION OF UV-VISIBLE SPECTROSCOPY
 Various components of a UV-Visible Spectroscopy

❖ Radiations source:

In visible – UV spectrometers, the most commonly used radiation sources are tungsten

halogen (or) deuterium arc lamp.

❖ Monochromators:

✓ The monochromators is used to disperse the radiation according to the wavelength.

✓ The essential elements of a monochromator are an entrance slit, a dispersing element and an

exit slit.

✓ The dispersing element may be a such as Prism and Holographic grating.

❖ Cells (sample cell and reference cell):
✓ The cells, cuvettes containing samples or reference for analysis should fulfil the following
conditions.
✓ They must be uniform in construction and the material of construction should be inert to
solvents.
✓ They must transmit the light of the wavelength.

❖ Detectors:

❖ Three common types of detectors are Barrier layer cell, Photomultiplier tube, Photocell used in

visible UV spectrophotometers.

❖ They converts the radiation, falling on which, into current as electrical signals. The current

is directly proportional to the concentration of the solution.

❖ Recording system:

❖ The signal from the detector is finally received by the recording system.

❖ The recording is done by recorder pen.

Working of visible and UV spectrophotometer:

❖ The radiation from the source is allowed to pass through the monochromator unit.

❖ The monochromator allows a narrow range of wavelength to pass through an exit slit.

❖ The beam of radiation coming out of the monochromator is split into two equal beams.
✓ One-half of the beam (the sample beam) is directed to pass through a transparent cell
containing a solution of the compound to be analysed.
✓ The half (the reference beam) is directed to pass through an identical cell that contains only the
solvent.

✓ The instrument is designed in such a way that it can compare the intensities of the two beams.

If the compound absorbs light at a particular wavelength, then intensity of the sample beam (I) will

be less than that of the reference beam (Io).

❖ The instrument gives output graph, which is a plot of wave length Vs absorbance of the light.

This graph is known as an absorption spectrum.

UV-VISIBLE SPECTROSCOPY- INSTRUMENTATION
 Applications
✓ Qualitative analysis: UV absorption spectroscopy is used for characterizing and identification of

aromatic compounds and conjugated olefins by comparing the UV absorption spectrum

of the sample with the same of known compounds available in reference books.

✓ Quantitative analysis: This determination is based on Beer‟s law. Where, € is molar extension

coefficient (constant), c is concentration, x is length of cell.

✓ Detection of impurities: UV absorption spectroscopy is the best method for detecting impurities in

organic compounds, because bands due to impurities are very intense and additional bands will obtained.

✓ Determination of molecular weight: Molecular weight of a compound can be determined if it can be

converted into a suitable derivative, which gives an absorption band.

✓ Dissociation Constants of acids and bases:

 IR spectroscopy
Principle
IR spectra is produced by the absorption of energy by a molecule in the
infrared region and the transitions occur between vibrational levels. So, IR
spectroscopy is also known as vibrational spectro scopy.

Range of Infrared Radiation

The range in the electromagnetic spectrum extending from 12500 to 50

cm−1(0.8 to 200 μ) is commonly referred to as the infrared. This region is
further divided into three sub regions.

I. Near infrared : the region is from 12500 to 4000 cm-1

II. Infrared (or) ordinary IR: The region is from 4000 to 667 cm-1
III. Far infrared: The region is from 667 to 50 cm-1.
Molecular Vibrations and Origin of IR Spectrum
Since atoms in a molecule are continuously vibrating, molecules are also vibrating. There
are two kinds of fundamental vibrations in the molecule.

❑ Stretching vibrations: During stretching the distance between two atoms decreases
or increases, but bond angle remains unaltered.

❑ Bending (or) deformation vibrations: During bending bond angle increases and
decreases but bond distance remains unaltered. Vibrational changes depend on the
masses of the atoms and their spatial arrangement in the molecule.
Group frequenices
 Finger Print Region :

The vibrational spectral (IR spectra) region at 1400 − 700 cm−1 gives very rich and

intense absorption bands. This region is termed as fingerprint region. The region

4000 − 1430 cm− 1 is known as Group frequency region.

Uses of fingerprint region

✓ IR spectra are often characterized as molecular finger prints, which detect the
presence of functional groups.
✓ Fingerprint region is also used to identify and characterize the molecule just as a
fingerprint can be used to identify a person.
 Instrumentation:

❑ Radiation Source:

The main source of IR Radiation: a). Nirchrome wire, b). Nernst glower, which is

filament containing Zr, Th. Ce held together with a binder. When they are heated

electrically at 1200 to 2000°C, they glow and produce IR radiation.

❑ Monochromator:

Diffracting grating or prism act as Monochromator. It allows the light of the required

wave length to pass through, but absorbs the light of other wave length.

❑ Sample Cell

The cell, holding the test sample, must be transparent to IR radiation.

❑ Thermal Detector

IR detectors generally convert thermal radiant energy into electrical energy. There are so

many detectors, of which the followings are important.

❖ Photoconductivity cell.

❖ Thermocouple.

❖ Pyroelectric detectors.

❑ Amplifiers and Recorders

The recorder records the signal coming out from the detector is amplified and registered by

a recorder.
Working of IR Spectrophotometer
The radiation emitted by the source is split into two identical beams having equal
intensity. One of the beams passes through the sample and the other through the
reference sample.
When the sample cell contains the sample, the half-beam travelling through it
becomes less intense.
When the two half beams (one coming from the reference and the other from the
sample) recombine, they produce an oscillating signal, which is measured by the
detector. The signal from the detector is passed to the recording unit and recorded.
Instrumentation
 Applications of IR spectroscopy

❑ Identity of the compound can be established

The IR spectrum of the compound is compared with that of known compounds. From the

resemblance of the two spectra, the nature of the compound can be established. This is

because a particular group of atoms gives a characteristic absorption band in the IR spectrum.
❑ Detection of impurity:

IR spectra of pure compound, presence of impurity can be detected.

❑ The secondary alcohol absorbs at 2.8 μ (~ 3570 cm− 1) due to O − H stretching. As the

reaction proceeds this band slowly disappears and a new band near 5.8 μ (~ 1725 cm− 1),

due to C = O stretching appears.

 ❑ Study of progress of a chemical reaction

The progress of a chemical reaction can be easily followed by examining the IR spectrum

of test solution at different time intervals.

❑ Determination of shape (or) Symmetry of a molecule

Whether the molecule is linear (or) non-linear (bend molecule) can be found out by IR

spectra.

Example: IR spectra of NO2 gives three peaks at 750, 1323, and 1616 cm− 1.
Computational chemistry- molecular dynamics and chemical reactivity

Computational chemistry is a branch of chemistry that uses computer simulations and

calculations to understand and predict the behavior of molecules and chemical systems.

Two important aspects of computational chemistry

1. Molecular Dynamics (MD)

2. Chemical Reactivity
Molecular Dynamics (MD):
Molecular dynamics is a computational technique that simulates the motion and

behavior of atoms and molecules over time. It is used to model the dynamics of a

system at the atomic and molecular level.

Components of molecular dynamics simulations:

➢ Force Fields:

Molecular dynamics simulations rely on force fields, which are mathematical descriptions of

the forces and interactions between atoms and molecules. These force fields define the potential

energy surface of the system.

➢ Integration Algorithms:

Molecular dynamics uses numerical integration methods, such as the Verlet algorithm, to

calculate the positions and velocities of atoms over time.

➢ Initial Conditions:

Simulations begin with a defined set of initial conditions, such as positions and velocities of

atoms.

➢ Boundary Conditions:

Simulations can be performed under different boundary conditions, including periodic boundary

conditions, to simulate systems of various sizes and shapes.

Applications of molecular dynamics in computational chemistry:

• Protein folding and dynamics.

• Behavior of materials at the atomic scale.

• Chemical reactions and reaction mechanisms.

• Properties of liquids, gases, and condensed phases.

 II. Chemical Reactivity:

Chemical reactivity in computational chemistry involves the study of how and why chemical

reactions occur, including the identification of reaction pathways, reaction mechanisms, and

the thermodynamics and kinetics of reactions.

Key aspects of the study of chemical reactivity

➢ Transition State Theory:

This theory explains the kinetics of chemical reactions by focusing on the transition state,

which is the highest-energy state along the reaction pathway.

➢ Reaction Coordinate:

The reaction coordinate is a mathematical representation of the progress of a chemical reaction.

It helps identify reactants, intermediates, and products and provides insights into reaction

mechanisms.
➢ Quantum Chemistry:

Quantum chemical calculations, such as density functional theory (DFT) and ab initio

methods, are used to determine the electronic structure and energy profiles of reactants

and products. These calculations are crucial for understanding reaction energetics.

➢ Free Energy Calculations:

Free energy calculations are used to predict reaction thermodynamics and kinetics,

including reaction rates.

Applications of the study of chemical reactivity in computational chemistry:

• Predicting reaction pathways and mechanisms.

• Studying the stability of chemical species.

• Calculating reaction energetics and kinetics.

• Designing new molecules and catalysts for specific reactions.

 DFT basics for chemical reactivity

❑ Schrodinger equation can be solved easily for one electron system.

❑ For muliple electron systems it is hard to solve the schrodinger equation.
So we introduce the approximation of density functional theory.
❑ DFT calculations are like ab-initio and semi-empirical calculations, based on
the schrodinger equation.
❑ However, unlike the other two methods, DFT does not calculate a conventional
wave function, but rather derives the electron distribution (electron density
function ) directly.
❑ Density functional calculations are usually faster than ab inito, but slower than
semiempirical.
❑ In DFT, the total energy is expressed in terms of the total electron density rather
than the wave function.
 Cheminformatics and Green IoT in biomedical applications

Cheminformatics in Biomedical Applications:

❑ Cheminformatics, a subfield of bioinformatics, focuses on the management and

analysis of chemical and biological data, with the goal of discovering valuable insights

for biomedical and pharmaceutical applications.

❑ Cheminformatics tools and techniques have significant implications for drug

discovery, toxicity prediction, and the understanding of molecular interactions.

 Applications of cheminformatics in the biomedical field:
➢ Drug Discovery:

Cheminformatics plays a pivotal role in identifying potential drug candidates. It involves the

analysis of chemical databases to find compounds that may exhibit therapeutic effects.

Computational methods are used to screen compounds, predict their pharmacokinetic properties,

and assess their interactions with biological targets.

➢ Toxicology Prediction:

Cheminformatics tools are used to assess the toxicity of chemical compounds. Predictive

models are developed to evaluate the safety of drugs, environmental pollutants, and other chemical

These models help in the early identification of potential hazards.

➢ Pharmacophore Modeling:
Cheminformatics techniques are used to build pharmacophore models, which describe the essential
features and spatial arrangement required for a compound to bind to a specific target. This aids in
virtual screening and drug design.
➢ Chemical Similarity and Clustering:

Cheminformatics allows for the comparison of chemical structures, facilitating the identification of

structurally similar compounds or clusters of related compounds. This can help in identifying lead

compounds or scaffold hopping.

➢ Chemical Informatics Databases:

Databases containing chemical information, such as PubChem and ChEMBL, are valuable

resources for researchers in drug discovery and medicinal chemistry.

➢ Polypharmacology:

The study of compounds that interact with multiple targets, known as polypharmacology, is an

emerging area of interest. Cheminformatics is used to explore the potential of drugs to target

multiple pathways and diseases simultaneously.

Green Internet of Things (IoT) in Biomedical Applications:

Green IoT in the context of biomedical applications refers to the use of IoT technologies

and devices to support sustainable, energy-efficient, and environmentally friendly

healthcare solutions. These applications aim to reduce energy consumption, minimize

waste, and improve overall healthcare services.

Some examples of green IoT in biomedical applications:

❑ Remote Patient Monitoring:

IoT devices can be used to monitor patients remotely, allowing for reduced hospitalization

and minimizing energy consumption associated with healthcare facilities.

❑ Energy-Efficient Hospital Operations:

IoT systems can optimize hospital operations by efficiently managing energy usage,

heating, cooling, and lighting to reduce environmental impact.

❑ Wearable Health Devices:

Wearable IoT devices, like fitness trackers and health monitors, help individuals manage their

health and fitness. These devices can be designed to use minimal energy and promote sustainability.

❑ Medication Adherence:

IoT-based smart medication dispensers and reminders can help patients adhere to their medication

schedules, reducing waste and the environmental impact of pharmaceuticals.

❑ Environmental Monitoring:

IoT sensors can be deployed to monitor environmental factors relevant to public health, such as air

quality, water quality, and disease vectors (e.g., mosquitoes in areas prone to diseases like malaria o

Zika virus).

❑ Telemedicine and Virtual Consultations:

reduce the need for physical travel to healthcare facilities, minimizing carbon emissions and energy
use.
Artificial intelligence and machine learning methods to predict physicochemical properties

➢ Artificial intelligence (AI) and machine learning (ML) methods have been increasingly

employed to predict physicochemical properties of molecules and materials.

➢ These methods are particularly useful in drug discovery, materials science, and other fields

where predicting properties can save time and resources.

➢ Some key AI and ML methods used for this purpose:

➢ Quantitative Structure-Property Relationship (QSPR) Models:

❑ QSPR models correlate the chemical structure of molecules with their

physicochemical properties. Features extracted from molecular structures, such as

atom types, bond types, and molecular descriptors, are used as inputs.

❑ Common algorithms used for QSPR modeling include multiple linear regression

(MLR), support vector machines (SVM), and artificial neural networks (ANN).
➢ Quantitative Structure-Activity Relationship (QSAR) Models:
QSAR models are a specific type of QSPR that focuses on predicting biological or chemical
activity, such as the binding affinity of a molecule to a target.
These models are widely used in drug discovery and toxicity prediction.
➢ Chemoinformatics and Molecular Descriptors:
❖ Machine learning models can be trained on a diverse set of chemical compounds, using
molecular descriptors as features. These descriptors capture various aspects of a molecule's
structure and properties.
❖ Random forests, decision trees, and gradient boosting algorithms are commonly used for
chemoinformatics modeling.
➢ Deep Learning and Neural Networks:
❖ Deep learning techniques, such as convolutional neural networks (CNNs) and recurrent
neural networks (RNNs), can be applied to molecular structures and representations to
predict physicochemical properties.
❖ Graph neural networks (GNNs) are particularly well-suited for modeling molecular
structures, as they can capture the connectivity of atoms and bonds.
➢ Transfer Learning:

Transfer learning leverages pre-trained models on large datasets to improve the

accuracy of property prediction for smaller datasets. Pre-trained models can capture

general chemical knowledge that is transferable to specific tasks.

➢ Ensemble Methods:

Ensemble methods combine the predictions of multiple models to enhance accuracy

and robustness. Techniques like random forests and gradient boosting are often used

in ensemble modeling.

➢ Quantum Mechanics (QM) and Molecular Dynamics Simulations:

While not traditional ML, QM and molecular dynamics simulations are used to

calculate physicochemical properties from first principles. These methods are

computationally intensive but provide high-accuracy predictions.

➢ Databases and Large-Scale Data Mining:

The availability of large databases of chemical and biological data enables data-

driven ML approaches. Researchers can mine these databases to build predictive

models.

➢ Biological and Chemical Data Integration:

ML models can combine biological and chemical data to predict properties that

result from complex interactions, such as drug-receptor binding affinity.

➢ Feature Engineering:

Feature engineering is the process of selecting or creating relevant features from

raw data to improve model performance. It is particularly important when dealing

with diverse chemical datasets.