Topic name: Introduction of Computational Chemistry
Group-D
Saidul Islam-08
Sharmin Akhter-10
Laila Rahman-21
Md. Yusuf Hossain-32
Shahin Alam-42
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Computational Chemistry
Computational chemistry is a branch of chemistry that utilizes computer
simulation and modelling techniques to understand and predict the behaviour of
chemical systems.
It involves the application of mathematical methods and algorithms to solve
complex problems in quantum mechanics, molecular dynamics, and statistical
mechanics.
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Area of Investigation in Computational Chemistry
Molecular Geometry:
Computational Chemistry investigates the shape of the molecules, bond
lengths, angles, and dihedrals.
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Area of Investigation in Computational Chemistry
Energies of molecules and Transition states:
This tells us which isomer is favoured at equilibrium and how fast a reaction
should go.
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Area of Investigation in Computational Chemistry
Chemical Rreactivity
Using Computational Chemistry we can investigate how readily or effectively
molecules undergo chemical reaction. For example, identifying electrophilic sites and
nucleophilic sites and predict where various kinds of reagents will attack a molecule.
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Area of Investigation in Computational Chemistry
Spectral Analysis (IR, UV & NMR)
Computational chemistry plays a
significant role in interpreting and
predicting results in various
spectroscopic techniques.
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Area of Investigation in Computational Chemistry
The interaction of substrate with enzyme
Computational chemistry plays a crucial role in studying how molecules fit into
active sites of an enzyme (one approach to design better drugs.)
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Tools of Computational Chemistry
Molecular Semiempirical
Mechanics Ab initio calculations
(MM) calculations
(SE)
Density Molecular
functional dynamics
calculations calculations
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(1) Molecular Mechanics
Molecular mechanics is a computational approach in theoretical chemistry that
simplifies the quantum mechanical description of molecules to make calculations
more computationally feasible. Molecular models are shown as a collection of
balls (atoms) held together by springs (bonds).
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(1) Molecular Mechanics (Contd.)
Geometry optimisation: Identifying the geometry of molecule (having lowest
energy) by changing the geometry until the lowest energy is calculated.
A large molecule (e.g. steroid like cholesterol C27H46O ) can be optimised in
seconds on a powerful desktop computer (a work station). It is the fastest method
in computational chemistry.
Cholesterol
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(2) Ab initio Calculations
• Ab initio is from the Latin: “from first principles”
• Based on Schrödinger equation.
The ab initio method solve Schrödinger equation for a
molecule and give energy and wavefunction.
Schrödinger Energy and Electron
equation wave function distribution
of
molecule
(2) Ab initio Calculations (Contd.)
• Ab initio Calculations are slow.
Geometry and spectra of simple molecule (propane ) can be calculated in minutes
on a premium type machine. But steroids take weeks!!
Propane
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(3) Semiempirical calculations
Based on Schrödinger equation (like ab initio) but parametrized with
experimental values (empirical=experimental).
Parameterization: The plugging of experimental values into a mathematical
procedure to get the best calculated value.
Mixing of theory and experimental (It makes method is “semiempirical”)
Here, more approximations are made in solving Schrödinger equation, and the very
complicated integrals (that must be calculated in ab initio methods are not actually
evaluated in Semi empirical calculations.
Instead, the program daws a library of integrals that was compiled by finding the best fit
of some calculated entity (eg: energy) to experimental value.
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(3) Semiempirical calculations (Contd.)
• Semi empirical calculations are slower than molecular mechanics but much
faster than ab initio calculations.
Ab initio Semiempirical Molecular
Calculations calculations
Mechanics
slow fast
Cholesterol Several Weeks On A minute on In seconds on
Geometry Pentium type premium type a desktop
Optimization machine machine computer
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(4) Density functional Calculations
Density functional theory is a quantum mechanical modelling approach used in
chemistry & physics to study the electronic structure of atoms and molecules. It’s
based on Schrödinger equation (like ab initio and semiempirical methods).
DFT does not calculate wavefunction but rather derives the electron distribution
(electron density function) directly.
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(4) Density functional Calculations (Contd.)
• DFT calculations are faster than ab initio but slower than
semiempirical calculations
Ab initio DFT Semiempirical Molecular
Calculations calculations calculations mechanics
SLOW FAST
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(5) Molecular Dynamics
• Molecular Dynamics is a simulation technique used in computational chemistry
to study the time dependant behaviour of a molecular system.
• It involves the numerical integration of Newton’s equations of motion to
simulate the movement of atoms and molecules over time.
• Thus, one can simulate the motion of an enzyme as it changes shape on binding
to a substrate, or the motion of a swarm of water molecules around a molecule
of solute.
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(5) Molecular Dynamics (Contd.)
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Uses of Computational Chemistry
• Pharmaceutical industry: to explore drug-biomolecule interactions & Drug
Discovery.
• Material science: properties of solids.
• Understanding Reaction Mechanism
• Predicting Molecular Structure
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Advantages & Disadvantages of Computational Chemistry
Advantages Disadvantages
Cost-effective Limited accuracy
Predictive power Computational power dependency
Environmentally safe Software dependency
Exploration of unstable species Need for experimental validation
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THANK YOU
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