Computational chemistry uses theoretical chemistry calculations incorporated into computer programs to calculate molecular structures and properties. It can calculate properties such as structure, energy, charge distribution, and spectroscopic quantities using methods ranging from highly accurate ab initio methods to less accurate semi-empirical and molecular mechanics methods. Computational chemistry has advantages like allowing medicinal chemists to measure molecular geometry, energies, and perform conformational analysis using computer power. It can also determine ligand and target structures through computational docking methods.
Basics of Quantum and Computational ChemistryGirinath Pillai
Basic fundamentals of theoretical, quantum and computational chemistry. The methods and approaches helps in predicting the electronic structure properties as well as other spectral data.
This presentation shows a technique of how to solve for the approximate ground state energy using Schrodinger Equation in which the solution for wave function is not on hand
In computational physics and Quantum chemistry, the Hartree–Fock (HF) method also known as self consistent method is a method of approximation for the determination of the wave function and the energy of a quantum many-body system or many electron system in a stationary state
(This presentation is in .pptx format, and will display well when embedded improperly, such as on the SlideShare site. Please download at your discretion, and be sure to cite your source)
Review of the Hartree-Fock algorithm for the Self-Consistent Field solution of the electronic Schroedinger equation. This talk also serves to highlight some basic points in Quantum Mechanics and Computational Chemistry.
March 21st, 2012
Computational Chemistry aspects of Molecular Mechanics and Dynamics have been discussed in this presentation. Useful for the Undergraduate and Postgraduate students of Pharmacy, Drug Design and Computational Chemistry
Basics of Quantum and Computational ChemistryGirinath Pillai
Basic fundamentals of theoretical, quantum and computational chemistry. The methods and approaches helps in predicting the electronic structure properties as well as other spectral data.
This presentation shows a technique of how to solve for the approximate ground state energy using Schrodinger Equation in which the solution for wave function is not on hand
In computational physics and Quantum chemistry, the Hartree–Fock (HF) method also known as self consistent method is a method of approximation for the determination of the wave function and the energy of a quantum many-body system or many electron system in a stationary state
(This presentation is in .pptx format, and will display well when embedded improperly, such as on the SlideShare site. Please download at your discretion, and be sure to cite your source)
Review of the Hartree-Fock algorithm for the Self-Consistent Field solution of the electronic Schroedinger equation. This talk also serves to highlight some basic points in Quantum Mechanics and Computational Chemistry.
March 21st, 2012
Computational Chemistry aspects of Molecular Mechanics and Dynamics have been discussed in this presentation. Useful for the Undergraduate and Postgraduate students of Pharmacy, Drug Design and Computational Chemistry
Molecular Mechanics in Molecular ModelingAkshay Kank
In this slide you learn about the computational chemistry and its role in designing a drug molecule. Also learn concept about the molecular mechanics and its application to Computer Aided Drug Design. difference between the Quantum mechanics and Molecular Mechanics.
IJERA (International journal of Engineering Research and Applications) is International online, ... peer reviewed journal. For more detail or submit your article, please visit www.ijera.com
IJERA (International journal of Engineering Research and Applications) is International online, ... peer reviewed journal. For more detail or submit your article, please visit www.ijera.com
Model Attribute Check Company Auto PropertyCeline George
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June 3, 2024 Anti-Semitism Letter Sent to MIT President Kornbluth and MIT Cor...Levi Shapiro
Letter from the Congress of the United States regarding Anti-Semitism sent June 3rd to MIT President Sally Kornbluth, MIT Corp Chair, Mark Gorenberg
Dear Dr. Kornbluth and Mr. Gorenberg,
The US House of Representatives is deeply concerned by ongoing and pervasive acts of antisemitic
harassment and intimidation at the Massachusetts Institute of Technology (MIT). Failing to act decisively to ensure a safe learning environment for all students would be a grave dereliction of your responsibilities as President of MIT and Chair of the MIT Corporation.
This Congress will not stand idly by and allow an environment hostile to Jewish students to persist. The House believes that your institution is in violation of Title VI of the Civil Rights Act, and the inability or
unwillingness to rectify this violation through action requires accountability.
Postsecondary education is a unique opportunity for students to learn and have their ideas and beliefs challenged. However, universities receiving hundreds of millions of federal funds annually have denied
students that opportunity and have been hijacked to become venues for the promotion of terrorism, antisemitic harassment and intimidation, unlawful encampments, and in some cases, assaults and riots.
The House of Representatives will not countenance the use of federal funds to indoctrinate students into hateful, antisemitic, anti-American supporters of terrorism. Investigations into campus antisemitism by the Committee on Education and the Workforce and the Committee on Ways and Means have been expanded into a Congress-wide probe across all relevant jurisdictions to address this national crisis. The undersigned Committees will conduct oversight into the use of federal funds at MIT and its learning environment under authorities granted to each Committee.
• The Committee on Education and the Workforce has been investigating your institution since December 7, 2023. The Committee has broad jurisdiction over postsecondary education, including its compliance with Title VI of the Civil Rights Act, campus safety concerns over disruptions to the learning environment, and the awarding of federal student aid under the Higher Education Act.
• The Committee on Oversight and Accountability is investigating the sources of funding and other support flowing to groups espousing pro-Hamas propaganda and engaged in antisemitic harassment and intimidation of students. The Committee on Oversight and Accountability is the principal oversight committee of the US House of Representatives and has broad authority to investigate “any matter” at “any time” under House Rule X.
• The Committee on Ways and Means has been investigating several universities since November 15, 2023, when the Committee held a hearing entitled From Ivory Towers to Dark Corners: Investigating the Nexus Between Antisemitism, Tax-Exempt Universities, and Terror Financing. The Committee followed the hearing with letters to those institutions on January 10, 202
Read| The latest issue of The Challenger is here! We are thrilled to announce that our school paper has qualified for the NATIONAL SCHOOLS PRESS CONFERENCE (NSPC) 2024. Thank you for your unwavering support and trust. Dive into the stories that made us stand out!
Introduction to AI for Nonprofits with Tapp NetworkTechSoup
Dive into the world of AI! Experts Jon Hill and Tareq Monaur will guide you through AI's role in enhancing nonprofit websites and basic marketing strategies, making it easy to understand and apply.
The French Revolution, which began in 1789, was a period of radical social and political upheaval in France. It marked the decline of absolute monarchies, the rise of secular and democratic republics, and the eventual rise of Napoleon Bonaparte. This revolutionary period is crucial in understanding the transition from feudalism to modernity in Europe.
For more information, visit-www.vavaclasses.com
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This presentation provides a briefing on how to upload submissions and documents in Google Classroom. It was prepared as part of an orientation for new Sainik School in-service teacher trainees. As a training officer, my goal is to ensure that you are comfortable and proficient with this essential tool for managing assignments and fostering student engagement.
The Roman Empire A Historical Colossus.pdfkaushalkr1407
The Roman Empire, a vast and enduring power, stands as one of history's most remarkable civilizations, leaving an indelible imprint on the world. It emerged from the Roman Republic, transitioning into an imperial powerhouse under the leadership of Augustus Caesar in 27 BCE. This transformation marked the beginning of an era defined by unprecedented territorial expansion, architectural marvels, and profound cultural influence.
The empire's roots lie in the city of Rome, founded, according to legend, by Romulus in 753 BCE. Over centuries, Rome evolved from a small settlement to a formidable republic, characterized by a complex political system with elected officials and checks on power. However, internal strife, class conflicts, and military ambitions paved the way for the end of the Republic. Julius Caesar’s dictatorship and subsequent assassination in 44 BCE created a power vacuum, leading to a civil war. Octavian, later Augustus, emerged victorious, heralding the Roman Empire’s birth.
Under Augustus, the empire experienced the Pax Romana, a 200-year period of relative peace and stability. Augustus reformed the military, established efficient administrative systems, and initiated grand construction projects. The empire's borders expanded, encompassing territories from Britain to Egypt and from Spain to the Euphrates. Roman legions, renowned for their discipline and engineering prowess, secured and maintained these vast territories, building roads, fortifications, and cities that facilitated control and integration.
The Roman Empire’s society was hierarchical, with a rigid class system. At the top were the patricians, wealthy elites who held significant political power. Below them were the plebeians, free citizens with limited political influence, and the vast numbers of slaves who formed the backbone of the economy. The family unit was central, governed by the paterfamilias, the male head who held absolute authority.
Culturally, the Romans were eclectic, absorbing and adapting elements from the civilizations they encountered, particularly the Greeks. Roman art, literature, and philosophy reflected this synthesis, creating a rich cultural tapestry. Latin, the Roman language, became the lingua franca of the Western world, influencing numerous modern languages.
Roman architecture and engineering achievements were monumental. They perfected the arch, vault, and dome, constructing enduring structures like the Colosseum, Pantheon, and aqueducts. These engineering marvels not only showcased Roman ingenuity but also served practical purposes, from public entertainment to water supply.
A Strategic Approach: GenAI in EducationPeter Windle
Artificial Intelligence (AI) technologies such as Generative AI, Image Generators and Large Language Models have had a dramatic impact on teaching, learning and assessment over the past 18 months. The most immediate threat AI posed was to Academic Integrity with Higher Education Institutes (HEIs) focusing their efforts on combating the use of GenAI in assessment. Guidelines were developed for staff and students, policies put in place too. Innovative educators have forged paths in the use of Generative AI for teaching, learning and assessments leading to pockets of transformation springing up across HEIs, often with little or no top-down guidance, support or direction.
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1. 01/23/181
COMPUTATIONAL CHEMISTRY
Computational chemistry uses result of theoretical chemistry
incorporated into efficient computer programmed to calculate
structure and properties of molecule.
It calculate the properties of molecule such as structure,
relative energy, charge distribution, dipole moment,
vibrational frequency, reactivity and other spectroscopic
quantity.
Computational chemistry range from highly accurate (Ab
initio method to less accurate (semiemiprical) to very
approximate (molecular mechanics).
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Advantage of Computational
Chemistry
1) It allows the medicinal chemist for use the
computational power of computer for measurement of
Mol. geometry
electron density
electrostatic potentional
conformational analysis
different types of energies.
2) Determination of structure of ligand and target through
X-ray crystallography and NMR spectroscopy.
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3) Docking of ligand in rececpter active sites and exact
measerment of geometric and energetic favor ability of
such interaction.
4) Comparssion of various ligands throgth various
parameters.
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What does Computational
Chemistry Calculate?
Energy, Structure and Properties
• What is the energy for a given geometry?
• How does energy vary when geometry changes?
• Which geometries are stable?
• How do atoms rearranges to form new molecules?
• How do stucture, energy, and properties change over time?
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What does Computational
Chemistry Calculate?
Examples
• Ionization energy (HOMO energy).
• Electron affinity (LUMO energy).
• Proton affinity.
• Electronic excitation energy (UV-Vis spectra).
• NMR chemical shifts and coupling constants.
• Reaction path and barrier height.
• Reaction rate.
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Molecular modeling method
The three dimensional shape of both ligand and target site
may be determined by X-ray crystallography or
computational method.
The most common computational methods are based on
either molecular or quantum mechanics.
Both this approaches produce equation for total energy of
the structure.
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Computational method
There are two main types method depending on the
starting point theory.
• Classical method :-
Are those method use Newton mechanics to model
molecular system.
• Quantum chemistry method:-
Which makes use of Quantum mechanics to model the
molecular system. This method used different type of
approximation to solve Schrödinger’s Equation.
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Classical Methods
1. Molecular Mechanics
2. Molecular Dynamics.
Quantum Mechanics Methods
1. Semi empirical Methods.
2. Ab initio Methods.
3. Density functional Theory.
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Molecular Mechanics
• Molecular mechanics programs use equations based
on classical physics to calculate force fields.
• Atoms treated as spheres, bonds as springs and electron
are ignored.
• It assume that the total potential energy (Etotal) of molecule
is given by sum of all the energies of attractive and
repulsive forces between atom in structure.
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The molecular mechanics equation
E = EB+EA+ED+ENB
EB = The energy involved in the
deformation bond either by
stretching or compression.
EA = The energy involved in the angle
bending .
ED = The torsional angle energy.
ENB = The energy involved in the interaction
between atoms that are not directly
bonded.
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Force Field
Force field refers to calculation of the interaction and
energies between different atoms between bond
stretching, angle bending, torsional angle and non-
bonded interaction.
Force field ignores the electronic distribution while
Quantum mechanics considers electronic distribution
of molecule.
13. 01/23/1813
Classical empirical force field
1) AMBER(Assisted Model Building and energy
Refinement)
2) CHRAM (Chemistry at Harvard Macromoleculer
Mechanics)
3) CVFF(Consistent Valence Force Field)
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Molecular Model Using Molecular
Mechanics
The molecular models are created by either using an existing
commercial force field computer program or assembling a
model from structural fragments held in the database of
molecular modeling program.
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Molecular Dynamics
• Molecular dynamics is a molecular mechanics program designed to
mimic the movement of atoms within a molecule.
• Molecular dynamics can be carried out o a molecule to generate
different conformation which on energy minimization, give a range
of stable conformation. Alternatively bonds can be rotated in a
stepwise process to generate different conformation.
• Molecular dynamics can also be used to find minimum energy
structures and conformational analysis.
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Quantum mechanics
• Quantum mechanics is based on arrangement of electrons
of molecule and interaction of those electron with
electron and nuclei of other molecule.
• It based on the realization that electron and all material
exhibit wavelike properties.
• The Quantum mechanics based on finding solution to
Schrödinger wave equation.
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Schrödinger’s Equation
The Schrödinger equation is the basis of quantum mechanics and gives a
complete description of the electronic structure of a molecule. If the
equation could be fully solved all information of a molecule could be
determined.
Hψ = Eψ
Where
H=Hamiltonian operator
Ψ =wave fuction
E =Energy system
To solve schrodinger equation was found to difficult. Hydrogen-total
energy of hydrogen (E) can be described as the sum of kinetic energy and
potential energy of its two component i.e. proton and electron.
20. 01/23/1820
Schrödinger equation for this relationship can written,
Hψ=(k+v)=Eψ
Where as
K = kinetic energy
V = potential energy
Describes both the wave and particle behavior of electrons.
The wave function is described by ψ while the particle behavior
is represented by E.
In systems with more than one electron, the wave function is
dependent on the position of the atoms; this makes it important to
have an accurate geometric description of a system.
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Ab Initio method
• Ab initio translated from Latin means from “first
principles”.
• This refers to the fact that no experimental data is used
and computations are based on quantum mechanics.
• It derived directly from theoretical principle.
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Hartree-Fock (HF)
• The simplest ab initio calculation.
• It based on Central field approximation.
• The major disadvantage of HF calculations is that
electron correlation is not taken into consideration.
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Density Functional Theory
• Considered an ab initio method, but different from other
ab initio methods because the wave function is not used
to describe a molecule.
• Density functional theory in which total energy is
expressed in term of total electron density is used.
• DFT methods take less computational time than HF
calculations and are considered more accurate.
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• Semi-empirical quantum methods, represents a middle
road between the mostly qualitative results available from
molecular mechanics and the high computationally
demanding quantitative results from ab initio methods.
• Semi empirical methods use experimental data to
parameterize equations.
• Like the ab initio methods, a Hamiltonian and wave
function are used.
• Less accurate than ab initio methods but also much faster.
• Capable of calculating transition states and excited states.
Semi Empirical Method
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Choice of Method
The method of calculation based on what calculation needs
to done and size of molecule.
Molecular mechanics useful for
Energy minimization
Identifying stable conformation
Energy calculation for specific conformations
Studying molecular motion
Studying different conformation.
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Quantum mechanics method are suitable for
calculating,
Molecular orbital energies
Heat formation for specific conformation
Dipole moment
Bond dissociation energy
Transition-state geometries and energies
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Computational Cost vs. Accuracy
Number
of Atoms
Accuracy
10 100 1000 10,000
Atom and Small
Molecules Large Compounds
and Nano-clusters Proteins,
DNA, RNA …
Quantum Mechanical
Methods
Molecular Mechanics
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Quantum Mechanics vs. Molecular
Mechanics
Quantum Mechanics
1. Correctly describes the
Bond- breaking
and Bond-forming
2. Application limited to
Hundreds of Atoms
Molecular Mechanics
1. Does not properly describe
the Bond-breaking and
Bond-forming
2. Can treat more than 10,000
Atoms
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Quantum mechanics Molecular mechanics
1) More expensive 1) Less expensive
1) More time 2) Less time
1) More computing power 3) Less computing power
4) Used for small molecule 4) Used for large molecule
5) It can calculate electronic
properties like electron density
5) It cannot calculate electronic
properties like electron density
6) Application limited to hundreds
of atom
6) Applicable to more than ten
thousands of atoms
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Energy minimization
• Energy minimization produces the nearest stable
conformation to the structure presented and not
necessarily the global conformation.
• Energy minimization involved alteration of bond length,
bond angle, torsion angle and non-bonded interaction .
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Moleculer mechanics energy
minimization
• Molecular mechanics is an approach of energy minimization
that find stable, low energy conformation by changing the
geometry of a structure.
Type of algorithms
1)Steepest Descent procedure
2)Conjugate gradient procedure
3)Newton –Raphson procedure
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Selection of energy minimization
algorithms
• The selection of energy minimization algorithms depends
on size of system and current state of optimization.
• When molecule having larger than 200 atoms then
conjugate gradient procedure.
• When molecule having less than 200 atoms then newton-
raphson procedure.
• When molecule having larger than 10Kcal/mol/A then
Steepest Descent.
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Computer graphics
In Moleculer modeling, data produced are converted as
visual image on a computer
Images displayed as,
Space fill model
Ball and stick model
CPK model
Mesh model
Ribbon model
37. 01/23/1837Mesh representation of Aspirin
Ball and stick model
Ribbon representation of
dihydrofolate reductase
Stick model CPK model