Chemistry 700
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Chemistry 700. Lectures. Resources. Grant and Richards, Foresman and Frisch, Exploring Chemistry with Electronic Structure Methods (Gaussian Inc., 1996) Cramer, Jensen, Ostlund and Szabo, Modern Quantum Chemistry (McGraw-Hill, 1982). Why is one interested in computational chemistry?.

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Chemistry 700

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Chemistry 700

Chemistry 700




  • Grant and Richards,

  • Foresman and Frisch, Exploring Chemistry with Electronic Structure Methods (Gaussian Inc., 1996)

  • Cramer,

  • Jensen,

  • Ostlund and Szabo, Modern Quantum Chemistry (McGraw-Hill, 1982)

Chemistry 700

Why is one interested in computational chemistry?

  • • experiments are expensive, and often indirect.

    • structure and property prediction is of great value.

  • We need to know where the electrons are to be able to predict how eg. light will affect them or whether they are ready to create bonds with other atoms/molecules.

  • Possible applications include:

  • 1. drug design.

  • 2. development of new materials.

Chemistry 700

  • There exist various approximation levels, the major being:

  • Molecular Dynamics – called also Molecular Mechanics – treats atoms as classical

  • objects, with interactions described by predetermined potentials, usually fitted

  • to some analytical functions. Major applications are to perform geometry

  • optimization and eg. study docking (how a small drug molecule can bind to a

  • molecular macromolecule). This approach allows to study systems consisting

  • of thousands of atoms but its quality is limited by the choice of the force

  • field/potential.

  • Ab-initio Theory starts from fundamental equations of quantum theory and works

  • is up from there. Since strict analytical formula exists for energies and other

  • system properties, many various properties can be computed, including MD

  • potentials and interaction with light or magnetic field. However, full quantum-

  • mechanical treatment is expensive and the systems studied are severely limited

  • in the size to tens or hundreds of atoms. This course is focused mostly on this

  • method.

Schr dinger equation

Schrödinger Equation

  • H is the quantum mechanical Hamiltonian for the system (an operator containing derivatives)

  • E is the energy of the system

  •  is the wavefunction (contains everything we are allowed to know about the system)

  • ||2 is the probability distribution of the particles

Hamiltonian for a molecule

Hamiltonian for a Molecule

  • Kinetic energy of the electrons

  • Kinetic energy of the nuclei

  • Electrostatic interaction between the electrons and the nuclei

  • Electrostatic interaction between the electrons

  • Electrostatic interaction between the nuclei

Solving the schr dinger equation

Solving the Schrödinger Equation

  • Analytic solutions can be obtained only for very simple systems

  • Particle in a box, harmonic oscillator, hydrogen atom can be solved exactly

  • Need to make approximations so that molecules can be treated

  • Approximations are a trade off between ease of computation and accuracy of the result

Expectation values

Expectation Values

  • for every measurable property, we can construct an operator

  • repeated measurements will give an average value of the operator

  • the average value or expectation value of an operator can be calculated by:

Variational theorem

Variational Theorem

  • the expectation value of the Hamiltonian is the variational energy

  • the variational energy is an upper bound to the lowest energy of the system

  • any approximate wavefunction will yield an energy higher than the ground state energy

  • parameters in an approximate wavefunction can be varied to minimize the Evar

  • this yields a better estimate of the ground state energy and a better approximation to the wavefunction

Born oppenheimer approximation

Born-Oppenheimer Approximation

  • The nuclei are much heavier than the electrons and move more slowly than the electrons

  • In the Born-Oppenheimer approximation, we freeze the nuclear positions, Rnuc, and calculate the electronic wavefunction, el(rel;Rnuc) and energy E(Rnuc)

  • E(Rnuc) is the potential energy surface of the molecule (i.e. the energy as a function of the geometry)

  • on this potential energy surface, we can treat the motion of the nuclei classically or quantum mechanically

Born oppenheimer approximation1

Born-Oppenheimer Approximation

  • freeze the nuclear positions (nuclear kinetic energy is zero in the electronic Hamiltonian)

  • calculate the electronic wavefunction and energy

  • E depends on the nuclear positions through the nuclear-electron attraction and nuclear-nuclear repulsion terms

  • E = 0 corresponds to all particles at infinite separation

Nuclear motion on the born oppenheimer surface

Nuclear motion on the Born-Oppenheimer surface

  • Classical treatment of the nuclei (e,g. classical trajectories)

  • Quantum treatment of the nuclei (e.g. molecular vibrations)

Hartree approximation

Hartree Approximation

  • Assume that a many electron wavefunction can be written as a product of one electron functions

  • If we use the variational energy, solving the many electron Schrödinger equation is reduced to solving a series of one electron Schrödinger equations

  • each electron interacts with the average distribution of the other electrons

Hartree fock approximation

Hartree-Fock Approximation

  • the Pauli principle requires that a wavefunction for electrons must change sign when any two electrons are permuted

  • the Hartree-product wavefunction must be antisymmetrized

  • can be done by writing the wavefunction as a determinant

Spin orbitals

Spin Orbitals

  • each spin orbital I describes the distribution of one electron

  • in a Hartree-Fock wavefunction, each electron must be in a different spin orbital (or else the determinant is zero)

  • an electron has both space and spin coordinates

  • an electron can be alpha spin (, , spin up) or beta spin (, , spin up)

  • each spatial orbital can be combined with an alpha or beta spin component to form a spin orbital

  • thus, at most two electrons can be in each spatial orbital

Fock equation

Fock Equation

  • take the Hartree-Fock wavefunction

  • put it into the variational energy expression

  • minimize the energy with respect to changes in the orbitals

  • yields the Fock equation

Fock equation1

Fock Equation

  • the Fock operator is an effective one electron Hamiltonian for an orbital 

  •  is the orbital energy

  • each orbital  sees the average distribution of all the other electrons

  • finding a many electron wavefunction is reduced to finding a series of one electron orbitals

Fock operator

Fock Operator

  • kinetic energy operator

  • nuclear-electron attraction operator

Fock operator1

Fock Operator

  • Coulomb operator (electron-electron repulsion)

  • exchange operator (purely quantum mechanical -arises from the fact that the wavefunction must switch sign when you exchange to electrons)

Solving the fock equations

Solving the Fock Equations

  • obtain an initial guess for all the orbitals i

  • use the current I to construct a new Fock operator

  • solve the Fock equations for a new set of I

  • if the new I are different from the old I, go back to step 2.

Hartree fock orbitals

Hartree-Fock Orbitals

  • for atoms, the Hartree-Fock orbitals can be computed numerically

  • the ‘s resemble the shapes of the hydrogen orbitals

  • s, p, d orbitals

  • radial part somewhat different, because of interaction with the other electrons (e.g. electrostatic repulsion and exchange interaction with other electrons)

Hartree fock orbitals1

Hartree-Fock Orbitals

  • for homonuclear diatomic molecules, the Hartree-Fock orbitals can also be computed numerically (but with much more difficulty)

  • the  ‘s resemble the shapes of the H2+ orbitals

  • , , bonding and anti-bonding orbitals

Lcao approximation

LCAO Approximation

  • numerical solutions for the Hartree-Fock orbitals only practical for atoms and diatomics

  • diatomic orbitals resemble linear combinations of atomic orbitals

  • e.g. sigma bond in H2

     1sA + 1sB

  • for polyatomics, approximate the molecular orbital by a linear combination of atomic orbitals (LCAO)

Basis functions

Basis Functions

  • ’s are called basis functions

  • usually centered on atoms

  • can be more general and more flexible than atomic orbitals

  • larger number of well chosen basis functions yields more accurate approximations to the molecular orbitals

Roothaan hall equations

Roothaan-Hall Equations

  • choose a suitable set of basis functions

  • plug into the variational expression for the energy

  • find the coefficients for each orbital that minimizes the variational energy

Roothaan hall equations1

Roothaan-Hall Equations

  • basis set expansion leads to a matrix form of the Fock equations

    FCi = iSCi

  • F – Fock matrix

  • Ci – column vector of the molecular orbital coefficients

  • I – orbital energy

  • S – overlap matrix

Fock matrix and overlap matrix

Fock matrix and Overlap matrix

  • Fock matrix

  • overlap matrix

Intergrals for the fock matrix

Intergrals for the Fock matrix

  • Fock matrix involves one electron integrals of kinetic and nuclear-electron attraction operators and two electron integrals of 1/r

  • one electron integrals are fairly easy and few in number (only N2)

  • two electron integrals are much harder and much more numerous (N4)

Solving the roothaan hall equations

Solving the Roothaan-Hall Equations

  • choose a basis set

  • calculate all the one and two electron integrals

  • obtain an initial guess for all the molecular orbital coefficients Ci

  • use the current Ci to construct a new Fock matrix

  • solve FCi = iSCi for a new set of Ci

  • if the new Ci are different from the old Ci, go back to step 4.

Solving the roothaan hall equations1

Solving the Roothaan-Hall Equations

  • also known as the self consistent field (SCF) equations, since each orbital depends on all the other orbitals, and they are adjusted until they are all converged

  • calculating all two electron integrals is a major bottleneck, because they are difficult (6 dimensional integrals) and very numerous (formally N4)

  • iterative solution may be difficult to converge

  • formation of the Fock matrix in each cycle is costly, since it involves all N4 two electron integrals



  • start with the Schrödinger equation

  • use the variational energy

  • Born-Oppenheimer approximation

  • Hartree-Fock approximation

  • LCAO approximation

Ab initio methods

Ab initio methods

1. The Hartree-Fock method (HF)

The hartree fock method

The Hartree-Fock method

We want to solve the electronic Schrödinger equation:

For this, we need to make some approximations

These will lead to the Hartree-Fock method (which is

the simplest ab initio method)

The hartree fock method1

The Hartree-Fock method

Approximation 1:

Decompose Y into a combination of molecular orbitals (MOs)

MO: one-electron wavefunction (fn)

However, this is not a good wavefunction, as

wavefunctions need to be antisymmetric: swapping the

coordinates of two electrons should lead to sign change

Good wavefunction:

The hartree fock method2

The Hartree-Fock method

The antisymmetry of the wavefunction can be achieved by

constructing the wavefunction as a Slater Determinant:

fi is a “spinorbital”: contains also the spin of the electron

The hartree fock method3

The Hartree-Fock method

Approximation 2:

The Hartree-Fock wavefunction consists

of a single Slater Determinant

(This implies that the electron-electron repulsion

is only included as an average effect => the

Hartree-Fock method neglects electron correlation)

The hartree fock method4

LCAO: Linear Combination of Atomic Orbitals

AO or basis function


expansion coefficients

The Hartree-Fock method

Approximation 3:

The MOs fi are written as linear combinations of

pre-defined one-electron functions (basis functions or AOs)

The hartree fock method5

How to obtain the optimal coefficients cmi?

The Hartree-Fock method

  • The Hartree-Fock wavefunction is a single Slater Determinant

  • The MOs in the Slater Determinant are expressed as

    linear combinations of atomic orbitals

  • The exact form of the wavefunction depends on the

    coefficients cmi

  • The Hartree-Fock method aims to find the

    optimal wavefunction

The hartree fock method6

“The energy calculated from an approximation to the true

wavefunction will always be greater than the true energy”

The Hartree-Fock method

Variation Principle

So, just find the coefficients cmi that give the lowest energy!

This leads to the Hartree-Fock equations, which can be

solved by the Self-Consistent Field (SCF) method

The hartree fock method7

The Hartree-Fock method

Approximations leading to the Hartree-Fock method

  • Start with the electronic Schrödinger equation

  • Decompose Y into a combination of MOs => antisymmetry

    imposed by using Slater Determinant wavefunctions

  • Wavefunction consists of a single Slater Determinant

  • MOs are linear combinations of AOs (which are predefined)

  • Variation principle to find optimal coefficients

The hartree fock method8

The Hartree-Fock method

The main weakness of Hartree Fock is that it neglects

electron correlation

In HF theory: each electron moves in an average field

of all the other electrons. Instantaneous electron-electron

repulsions are ignored

Electron correlation: correlation between the spatial

positions of electrons due to Coulomb repulsion

- always attractive!

Post-HF methods include electron correlation

Ab initio methods1

Ab initio methods

Post-HF methods



Perturbation theory

(MP2, MP3, MP4,…)



Coupled Cluster



Interaction (CI)

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