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Chem. 141 Chem. 141
Dr. Mack Dr. Mack
An Overview of Computational Chemistry An Overview of Computational Chemistry
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Theoretical Chemistry:
The mathematical description of chemistry
A mathematical method that is sufficiently well developed
that it can be automated for implementation on a
computer.
Computational Chemistry:
Chemical Problems
Computer Programs
Physical Models
Math formulas
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Note that the words exact and perfect do not appear in
these definitions.
Computational chemistry is based on a approximations Computational chemistry is based on a approximations
and assumptions. and assumptions.
Only a real experimental measurement can approach the Only a real experimental measurement can approach the
limits of exactness! limits of exactness!
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What does Computational
Chemistry Calculate?
Energy, Structure, and Properties
Molecular Geometries:
What is the energy for a given geometry?
How does energy vary when geometry changes?
Which geometries are stable?
How does energy change w/r extenal
perturbation?
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Enthalpies of formation
Dipole moment
Orbital energy levels (HOMO, LUMO, others)
Ionization energy (HOMO energy)
Electron affinity (LUMO energy)
Electron distribution (electron density)
Electrostatic potential
Vibrational frequencies and normal modes (IR
spectra)
Electronic excitation energy (UV-Vis spectra)
NMR chemical shifts and coupling constants
Reaction path and barrier height
Reaction rate
What else can be computed:
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What can one learn from computational What can one learn from computational calculations calculations? ?
Molecular Visualization (Graphic Representation)
Molecular Mechanics (Classical Newtonian Physics)
Semi-empirical Molecular Orbital Theory
Ab Initio Molecular Orbital Theory
Density Functional Theory
Geometry Optimization
Molecular Dynamics
Quantum
Mechanical
Methods
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Molecular Mechanics (MM)
Empirical energy functions parameterized against experimental
dataFast, simple, generally not very accurate (> 10
4
atoms)
Semi-empirical Molecular Orbital (MO) Methods
Can treat moderate sized molecules (> 10
2
atoms).
Accuracy depends on parameterization.
Ab-initio Molecular Orbital Methods
Computationally demanding (> 10 atoms)
Accuracy can be systematically improved.
Density Function Theory (DFT)
More efficient than ab-initio calculations (> 10 atoms)
Accuracy varies, however, there is no systematical way to improve
the accuracy.
Types of Calculations:
I will focus on I will focus on
these topics these topics
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Types of Computational Calculations:
The term "Ab Initio" is latin for "from the beginning". "from the beginning". Ab AbI nitio I nitio: :
Computations of this type are derived directly from
theoretical principles, with no inclusion of experimental data.
Mathematical approximations are usually a simple functional
form for a an approximate solution to a differential equation.
A wave function! A wave function! (The (The Shr Shr dinger dinger Equation) Equation)
The most common type of ab initio calculation is called a
Hartree Hartree- -Fock Fock calculation.
The ? of complicated system (molecule molecule) is generated from a
linear combination of simple functions (basis set).
The parameters for the SE are varied until the solution (energy of energy of
the system the system) is optimized.
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Ab initio electronic structure theory
Hartree-Fock (HF)
Electron Correlation (MP2, CI, CC, etc.)
Molecular
properties
Geometry
prediction
Benchmarks for
parameterization
Transition States
Reaction coords.
Spectroscopic
observables
Prodding
Experimentalists
Goal: Insight into chemical phenomena.
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Setting up the problem
What is a molecule?
A molecule is composed of atoms, or, more generally as a collection of
charged particles, positive nuclei and negative electrons.
The interaction between charged particles is described by;
Coulomb Potential
Coulomb interaction between these charged particles is the only
important physical force necessary to describe chemical phenomena.
V
ij
=V(r
ij
) =
q
i
q
j
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0
r
ij
=
q
i
q
j
r
ij
r
ij
q
i
q
j
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But, electrons and nuclei are in constant
motion
In Classical Mechanics, the dynamics of a system (i.e. how the
system evolves in time) is described by Newtons 2nd Law:
F = ma
F = force
a = acceleration
r = position vector
m = particle mass

dV
dr
= m
d
2
r
dt
2
In Quantum Mechanics, particle behavior is described in terms of a
wavefunction, Y.


H = ih

t
Hamiltonian Operator

H
Time-dependent Schrdinger Equation

i = 1;h = h 2
( )
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Time-Independent Schrdinger Equation
If H is time-independent, the time-
dependence of Y may be separated out
as a simple phase factor.

H (r, t) =

H (r)
(r, t) = (r)e
iEt / h

H (r)(r) = E(r) Time-Independent Schrdinger Equation
Describes the particle-wave duality of electrons.
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Hamiltonian for a system with N-particles
Sum of kinetic (T) and potential (V)
energy

H =

T +

V


T =

T
i
=
h
2
2m
i i=1
N

i=1
N

i
2
=
h
2
2m
i i=1
N

2
x
i
2
+

2
y
i
2
+

2
z
i
2

i
2
=

2
x
i
2
+

2
y
i
2
+

2
z
i
2





Laplacian operator
Kinetic energy

V = V
ij
j>1
N

i=1
N

=
q
i
q
j
r
ij j >1
N

i=1
N
Potential energy
(Coulombic)
When these expressions are used in the time-independent Schrodinger
Equation, the dynamics of all electrons and nuclei in a molecule or atom
are taken into account.
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Born-Oppenheimer Approximation
Since nuclei are much heavier than electrons, their velocities are much
smaller. To a good approximation, the Schrdinger equation can be
separated into two parts:
One part describes the electronic wave function for a fixed nuclear
geometry.
The second describes the nuclear wave function, where the
electronic energy plays the role of a potential energy.

H =

T
n
+

T
e
+

V
ne
+
+

V
ee
+

V
nn
n = nuclear
e = electronic
ne = nucleus-electron
ee = electron-electron
nn = nucleus-nucleus
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Since the motions of the electrons and nuclei are on different time
scales, the kinetic energy of the nuclei can be treated separately. This
is the Born-Oppenheimer approximation. As a result, the electronic
wave function depends only on the positions of the nuclei.
Physically, this implies that the nuclei move on a potential energy
surface (PES), which are solutions to the electronic Schrdinger
equation. Under the BO approx., the PES is independent of the
nuclear masses; that is, it is the same for isotopic molecules.
Solution of the nuclear wave function leads to physically meaningful
quantities such as molecular vibrations and rotations.
0
E
H H
H
.
+ H
.
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Limitations of the Born-Oppenheimer approximation
The total wave function is limited to one electronic surface, i.e. a
particular electronic state.
The BO approx. is usually very good, but breaks down when
two (or more) electronic states are close in energy at particular
nuclear geometries.
In such situations, a non-adiabatic wave function - a product
of nuclear and electronic wave functions - must be used.
The electronic Hamiltonian becomes,

H =

T
e
+

V
ne +
+

V
ee
+

V
nn
B.O. approx.; fixed nuclear coordinates
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Hartree-Fock Self-consistent Field (SCF) Theory
GOAL: Solve the electronic Schrdinger equation, H
e
=E .
PROBLEM:
Exact solutions can only be found for one-electron systems, e.g., H
2
+
.
SOLUTION:
Use the variational principle to generate approximate solutions.
Variational principle
If an approximate wave function is used in H
e
=E , then the
energy must be greater than or equal to the exact energy.
The equality holds when is the exact wave function.
In practice:
Generate the best trial function that has a number of adjustable
parameters.
The energy is minimized as a function of these parameters.
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The energy is calculated as an expectation value of the Hamiltonian operator:
E =
|

H
e
|
|
If the wave functions are orthogonal and normalized (orthonormal),

i
|
j
=
ij

ij
= 1

ij
= 0
Then,
E = |

H
e
|
(Kroenecker delta)

H =

T
e
+

V
ne +
+

V
ee
+

V
nn
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assume that a many electron wave function can be
written as a product of one electron functions
Use the variational method energy, solving the many
electron Schrdinger equation is reduced to solving a
series of one electron Schrdinger equations
In this approximation, each electron interacts with the
average distribution of the other electrons
L L ) ( ) ( ) ( ) , , , (
3 2 1 3 2 1
r r r r r r =
Hartree Hartree Approximation Approximation
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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 wave function will yield an energy higher
than the ground state energy
parameters in an approximate wave function can be varied to
minimize the E
var
this yields a better estimate of the ground state energy and a
better approximation to the wave function
exact
E E
d
d
=

var
*
*

H
Variational Variational Theorem Theorem
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Since electrons are fermions, S = 1/2, the total electronic wave
function must be antisymmetric (change sign) with respect to the
interchange of any two electron coordinates. (Pauli principle - no
two electrons can have the same set of quantum numbers.)
1,2 ( ) =
1
(1)
2
(2)
1
(2)
2
(1)
Each electron resides in a spin-orbital, a product of spatial
and spin functions.
(Spin functions are orthonormal: | = | =1; | = | = 0)
2,1 ( ) =
1
(2)
2
(1)
1
(1)
2
(2)
2,1 ( ) = 1,2 ( )
Interchange the coordinates of the two electrons,
I spin-orbit wave function
= spin up state and = spin down state (for electrons 1 & 2)
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A more general way to represent antisymmetric electronic wave functions is in the
form of a determinant. For the two-electron case,
1,2 ( ) =

1
(1)
2
(1)

1
(2)
2
(2)
=
1
(1)
2
(2)
1
(2)
2
(1)
For an N-electron N-spinorbital wave function,

SD
=

1
1 ( )
2
(1) L
N
(1)

1
2 ( )
2
(2) L
N
(2)
L L L L

1
N ( )
2
(N) L
N
(N)
,
i
|
j
=
ij
A Slater Determinant (SD) satisfies the antisymmetry requirement.
Columns are one-electron wave functions, molecular orbitals.
Rows contain the electron coordinates.
One more approximation: The trial wave function will consist of a single SD.
Now the variational principle is used to derive the Hartree-Fock equations...
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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
n
L
2 1
=

d
d
E
*
*
var

H
i i i
= F

0 /
var
=
i
E
Fock Fock Equation Equation
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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 wave function is reduced to
finding a series of one electron orbitals
i i i
= F

K J V T F

+ + =
NE
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2
2
2

=
e
m
h
T

=
nuclei
A
iA
A
ne
r
Z e
2

V
nuclear-electron attraction operator
kinetic energy operator
K J V T F

+ + =
NE
Coulomb operator (electron-electron repulsion)
i j
ij
j
electrons
j
i
d
r
e
} {

= J
exchange operator
(antisymmetry requirement)
j i
ij
j
electrons
j
i
d
r
e
} {

= K
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1. obtain an initial guess for all the orbitals
i
2. use the current
I
to construct a new Fock operator
3. solve the Fock equations for a new set of
I
4. if the new
I
are different from the old
I
, go back to step 2.
5. When the values converge (do not change to a prescribed
limit), the calculation is complete.
i i i
= F

Solving the Solving the Fock Fock Equations Equations

i
=
i
' |

F
i
|
i
' The results are interpreted as MO energies.
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Hartree-Fock orbitals ( s ) can be computed numerically
for atoms
These resemble the shapes of the hydrogenic orbitals (s, p, d
and f)
for homonuclear diatomic molecules, the Hartree-Fock
orbitals resemble the MOs for species like H
2
+
, , bonding and anti-bonding orbitals
Hartree-Fock Orbitals
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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 H
2
1s
A
+ 1s
B
for polyatomics, approximate the molecular orbital by a
linear combination of atomic orbitals (LCAO)

c
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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

c
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Basis Set Approximation
For atoms and diatomic molecules, numerical HF methods
are available.
In most molecular calculations, the unknown MOs are
expressed in terms of a known set of functions - a basis set.
Two criteria for selecting basis functions.
I) They should be physically meaningful.
ii) computation of the integrals should be tractable.
It is common practice to use a linear expansion of Gaussian
functions in the MO basis because they are easy to handle
computationally.
Each MO is expanded in a set of basis functions centered at
the nuclei and are commonly called Atomic Orbitals.
(Molecular orbital = Linear Combination of Atomic Orbitals -
LCAO).
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Basis functions approximate orbitals of atoms in molecule
Linear combination of basis functions approximates total
electronic wave function
Basis functions are linear combinations of Gaussian functions
Contracted Gaussians
Primitive Gaussians
Basis sets
STOs vs. GTOs
Slater-type orbitals (J.C. Slater)
Represent electron density well in valence region and beyond
(not so well near nucleus)
Evaluating these integrals is difficult
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Gaussian-type orbitals (F. Boys)
Easier to evaluate integrals, but dont represent electron density
well
This can be overcome this by using linear combination of GTOs
One basis function for every atomic orbital required to
describe the free atom
Most-common: STO-3G
Linear combination of 3 Gaussian-type orbitals fitted to
one Slater-type orbital
CH
4
: H(1s); C(1s,2s,2p
x
,2p
y
,2p
z
)
Minimal basis set
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More basis functions per atom
Split valence basis sets
Double-zeta: Triple-zeta:
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Add more basis functions per atom
allow orbitals to change size
Add polarization functions
allow orbitals to change shape
Add diffuse functions for electrons with large radial extent
Add high angular momentum functions
Ways to increase a basis set
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Ab Initio (latin, from the beginning) Quantum
Chemistry Summary of approximations
Born-Oppenheimer Approx.
Non-relativistic Hamiltonian
Use of trial functions, MOs, in the variational procedure
Single Slater determinant
Basis set, LCAO-MO approx.
Consequence of using a single Slater determinant and
the Self-consistent Field equations:
Electron-electron repulsion is included as an average effect. The electron
repulsion felt by one electron is an average potential field of all the others,
assuming that their spatial distribution is represented by orbitals. This is
sometimes referred to as the Mean Field Approximation.
Electron correlation has been neglected!!!
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How does one know what to use when?
Considerations:
Computational resources
Molecule size
Kind of chemical question
Desired accuracy
Recommendations from literature
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Literature
Books
F. Jensen, Introduction to Computational
Chemistry, Wiley, 1999 (our textbook)
A. R. Leach, Molecular Modelling, 2nd Ed.,
Prentice Hall, 2001
C. J. Cramer, Essentials of Computational
Chemistry, 2nd Ed., Wiley, 2004
There are more, but these three should be good at the beginning.