1

An I nt r oduc t i on t o
Comput at i onal
Chemi st r y Labor at or y
An I nt r oduc t i on t o
Comput at i onal
Chemi st r y Labor at or y
2
What i s Comput at i onal Chemi st r y
Labor at or y (CCL)?

CCL is a virtual chemistry laboratory (in many cases
substitutes a real laboratory.)

The aim: use of computers to aid chemical inquiry. Based on:

Physical background

theory (Classical Newtonian or
Quantum Physics)

Mathematical numerical algorithms (optimization, linear
algebra, iteration procedures, numerical integration etc.)

Computer software and hardware (HYPERCHEM 8.0,
GAUSSIAN03 on Windows PC)

Chemical knowledge and intuition for understanding and
interpretation of the computational results
3
Pot ent i al Ener gy Sur f ac e (PES) t he mai n
c hemi st r y i nqui r y
Chemi st r y i s k now i ng t he ener gy as a f unc t i on of nuc l ear c oor di nat es F. J ensen
4
Pot ent i al ener gy sur f ac es (and
si mi l ar pr oper t i es) c al c ul at i on

Classical (Molecular) Mechanics

quick, simple; accuracy depends on parameterization; no

consideration of electrons interaction)

Quantum Mechanics:
1.

Molecular Wave Function Theory

Ab initio molecular orbital methods...much more demanding
computationally, generally more accurate.

Semi-empirical molecular orbital methods ...computationally
less demanding than ab initio, possible on a pc for moderate
sized molecules, but generally less accurate than ab initio,
especially for energies.
2.

Density functional theorymore efficient and often more
accurate than Wave Function based approaches.
5
Mol ec ul ar Mec hani c s a t heor y
of mol ec ul es w i t hout el ec t r ons

Employs classical
(Newtonian) physics

Assumes Hookes Law
forces between atoms
(like a spring between
two masses)
E
E
stretch stretch

=
=
k
k
s s

(l
(l
-
-

l
l
o o

)
)
2 2
graph:
graph:
C
C
-
-
C
C
;
;
C=O
C=O

Force field = {
k
k
s s

}
}
6
Mol ec ul ar Mec hani c s
Mor e el abor at e For c e Fi el ds (FF)
7
Bi r t h of quant um c hemi st r y
Wave pr oper t i es of mat t er
Bi r t h of quant um c hemi st r y
Wave pr oper t i es of mat t er

Prince Louis de Broglie (1923):

=

h/mv= h/p
h= 6.62607550D
-34
Js

p

=e
-i2x/
= e
-i2px/h
(wave-particle duality

paradox)

-

probabilistic (statistic) wave.
Waves properties: interference, diffraction etc.

Possible explanation:
The probabilistic behavior of elementary particles are
connected with structure of quantum vacuum.
8
Basi s of Quant um Chemi st r y
Basi s of Quant um Chemi st r y

Postulate I : A closed system is fully described by

Postulate II: Operator

for every physical quantity
(-ih/2t)d/dx (e
-i2px/h
) =

p (e
-i2px/h
)
(-ih/2t)d/dx

(
p

) =

p

(
p

)

Schrdinger equation (1926):
(can be solved exactly for the Hydrogen atom, but nothing larger)
P.A.M. Dirac, 1929: The underlying physical laws necessary for the
mathematical theory of a large part of physics and the whole of
chemistry are thus completely known.
d
i H E
dt
+
| |
= + = +
|
\ .

9
One-di mensi onal Sc hr di nger w ave
equat i on
2
2
2
2
2 2
2
2 2
2
2 2
2

Total energy kinetic potential

1
2 2

then

2
2
H E
p
mv V V
m
d
p i p pp
dx
d d d
p i i
dx dx dx
d
H V
m dx
d
V E
m dx

=
= +
= + = +
| |
= =
|
\ .
| | | |
= =
| |
\ . \ .
+
+ =

Hamiltonian operator
=operator of energy
SE =energy eigen-value equation

Extracts total energy, E

Many solutions

E
0

, E
1

,

E
n

+(x)

wavefunction

No direct physical meaning

,+

(x)|
2

Probability of
finding particle with
energy E at point x
Single-valued, finite, continuous
10
Mol ec ul ar
Sc hr di nger equat i on (SE):
E
1
M
A
2
A
_
h
2
8t
2
H
=
E
2
a
_
h
2
8t
2
m
electrons
A
>
nuclei
a
E
Z
A
r
Aa
_
e
2
E
nuclei electrons
a
A
E
Z
A
Z
B
r
AB
e
2
E
nuclei
A
E
1
r
ab
e
2
E
electrons
b
a
B >
+ +
kinetic energy (nuc.) kinetic energy (elect.)
2 kinetic energy terms plus
3 Coulombic energy terms:
(one attractive, 2 repulsive)
H+ = E+
H = Hamiltonion operator
11
Rel at i vi st i c quant um mec hani c s
Di r ac equat i on (1928) :
12
I nf l uenc e of Rel at i vi t y on
Quant um Wor l d and vi c e-ver sa
(x)
(x)
( )
(x)
(x)
L
L
S
S
x
o
|
o
|
| |
+
|
+
|
+ =
|
+
|
|
+
\ .
REALITY IS RELATIVISTIC AND THUS IS QUANTUM (and vice-versa!)
13
Di r ac s sea of el ec t r ons.
Quant um vac uum.
14
The NR mol ec ul ar w avef unc t i on
physi c al meani ng

The wavefunction, + , is a key quantity in quantum chemistry.

+ depends on coordinates and spins. Spin of electron

relativistic
property, additional discrete

coordinate ; |m
s1

|=1/2

In a three dimensional system of n-electrons,
is the probability of simultaneously
finding electron 1 with spin m
s1

in the volume dx
1

dy
1

dz
1

at (x
1

,y
1

,z
1

),
electron 2 with spin

m
s2

in the volume dx
2

dy
2

dz
2

at (x
2

,y
2

,z
2

)

and so on

The wave function should be normalized, that is, the probability

of
finding all electrons somewhere in space equals 1.
( )
2
1 1 1 1 1
,..., , ,..., ....
n s sn n n n
x z m m dx dy dz dx dy dz
( )
2
1 1 1 1 1 1

... , , ,..., , , ... 1
n n n n n n
all m
x y z x y z dx dy dz dx dy dz


=

} } } } }
15
Wavef unc t i ons gener al
pr oper t i es

The wave function should be antisymmetric, that is, + should
change sign when two electrons of the molecule interchange:

We can use the molecular wavefunction to calculate any
property of the molecular system. The average value, <C>,

of a
physical property of our molecular system is:

where, , is the quantum mechanical operator of the physical
property and

*

C C d C t =
}
1 1 1

... ...
n n n
all m
dx dy dz dx dy dz dt


=

} } } } }
( )
( )
1 1 1 ,..., 1
1 1 1 1
, , ,..., , , , , ,..., , , , ,...,
, , ,..., , , ,..., , , ,..., , , , ,...,
i i i j j j n n n s sn
j j j i i i n n n s sn
x y z x y z x y z x y z m m
x y z x y z x y z x y z m m

16
Ab-i ni t i o Wavef unc t i on appr oac h
Ab-i ni t i o Wavef unc t i on appr oac h

Simplifying assumptions are employed to solve

the Schrdinger equation approximately:

Born-Oppenheimer approximation

allows separate
treatment of nuclei and electrons

Hartree-Fock independent electron approximation

allows each electron to be considered as being
affected by the sum (field) of all other electrons.

LCAO Approximation

Tools: Variational

Principle or Perturbation
Theory
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Bor n-Oppenhei mer
Appr ox i mat i on -
E
1
M
A
2
A
_
h
2
8t
2
H
=
E
2
a
_
h
2
8t
2
m
electrons
A
>
nuclei
a
E
Z
A
r
Aa
_
e
2
E
nuclei electrons
a
A
E
Z
A
Z
B
r
AB
e
2
E
nuclei
A
E
1
r
ab
e
2
E
electrons
b
a
B >
+ +
kinetic energy (nuc.) kinetic energy (elect.)
1 kinetic energy term plus
2 Coulombic energy terms:
(one attractive, 1 repulsive)
plus a constant for nuclei
constant
18
St eps of sol ut i on of t he Sc hr di nger
equat i on i n t he Bor n-Oppenhei mer
appr ox i mat i on:
H
tot

= (T
n

+ V
n

)

+ T
e

+ V
ne

+ V
e

= (H
n

)

+ H
e
1.

Electronic SE: H
e

e

(r,R)=E
e

(R)
e

(r,R)
2.

Nuclear SE: (T
n

+ V
n

+ E
e

(R) )
n

(R)=E
n

n

(R)
V
n

+ E
e

(R)

= potential energy surface (PES)
TOTAL WF

: (r,R) =
n

(R)
e

(r,R)
In our laboratory we concentrate mainly on
solution of the electronic SE and working with PES
(finding minimums, transition states etc.)
19
Sol vi ng t he El ec t r oni c SE:
Har t r ee-Foc k (HF) appr ox i mat i on
t he physi c al bac k gr ound
Sol vi ng t he El ec t r oni c SE:
Har t r ee-Foc k (HF) appr ox i mat i on
t he physi c al bac k gr ound

Multi-electronic SE: H
e

e

(r,R)=E
e

(R)
e

(r,R)

is still very
complicated reduce it to the single-electronic equation

HF assumes that each electron experiences all the others
only as a whole (field of charge) rather than individual
electron-electron interactions.

Instead of multielectronic

Shrdinger

equation introduces
a one-electronic

Fock operator F:
F | = c |
which is the sum of the kinetic energy of an electron, a
potential that one electron would experience for a fixed
nucleus, and an average of the effects of the other
electrons.
20
Mat hemat i c al f oundat i on of t he HF (or
Sel f -c onsi st ent -f i el d (SCF)) met hod

Molecular orbital theory approximates the molecular wave function

as a antisymmetrized

product of orthonormal

one-electron
functions (or molecular spin-orbitals)

where

is the antisymmetrization

operator and

where k=1/2; o
1/2
=

; o
-1/2

=

.

The antisymmetrization

operator is defined as the operator that
antisymmetrizes

a product of n one-electron functions and
multiplies them by normalization factor (n!)
-1/2
1 2

( .... )
n
A f f f =
( , , )
i i i i i k
f x y z | o =
21
Det er mi nant of Sl at er

The antisymmetrized

WF can be
represented as the Slaters determinant:
( )
1 1 1 1 2 1 2 1 /2 1
1/2
1 2 1 2 2 2 2 2 /2 2
1 1 2 2 /2
( ) (1) ( ) (1) ( ) (1) ( ) (1) ... ( ) (1)
( ) (2) ( ) (2) ( ) (2) ( ) (2) ... ( ) (2)
!
... ...
( ) ( ) ( ) ( ) ( ) ( ) ( ) ( ) ... ( ) ( )
n
n
n n n n n n
x x x x x
x x x x x
n
x n x n x n x n x n
| o | | | o | | | |
| o | | | o | | | |
| o | | | o | | | |

+=



22
Var i at i onal Pr i nc i pl e

The energy E

calculated from any

approximation
of the wavefunction

will be higher

than the true
energy E
0

:

The better the wavefunction, the lower the energy
(the more closely it approximates reality).

Changes (variation of parameters in ) are made
systematically to minimize the calculated energy.

At the energy minimum (which approximates the
true energy of the system), dE/d
i

= 0.
*
0

E H d E t = u u >
}
23
The Har t r ee-Foc k ener gy
f unc t i onal

We shall restrict ourselves to closed shell configurations, for
such cases, a single Slater determinant is sufficient to describe
the molecular wave function. Using the variational

principle
within this framework lead to the restricted HF theory. The
Hartree-Fock energy for molecules with only closed shells is
/2 /2 /2
1 1 1
1
2 (2 )
2
n n n
core
HF i ij ij
i i j
E H J K
= = =
= +

2
1 1
1

(1) (1) (1) (1) / (1)

2
core core
i i i i I I i
I
H H Z r | | | | = V

12 12
(1) (2)1/ (1) (2) , (1) (2)1/ (1) (2)
ij i j i j ij i j j i
J r K r | | | | | | | |
24
The Har t r ee-Foc k equat i ons

The Hartree-Fock equations are derived from
the variational

principle, which looks for those
orbitals

that minimize E
HF

.

For computational convenience the molecular
orbitals are taken to be orthonormal:

The orthogonal Hartree-Fock molecular orbitals
satisfy the single-electronic equations:
(1)| (1)
i j ij
| | o =

(1) (1) (1)

i i i
F | c | =
25
The (Har t r ee-) Foc k oper at or

Single-electronic operator:

The Coulomb operator J
j

and the exchange
operator K
j

are defined by

where

f is an arbitrary function
/2
2
1 1
1
1

(1) / 2 (1) (1)
2
n
I I j j
I j
F Z r J K
=
(
= V +


2
2
12
*
2
12
1

(1) (1) (1) (2)

(2) (2)

(1) (1) (1)

j j
j
j j
J f f dv
r
f
K f dv
r
|
|
|
=
=
}
}
26
Nex t st ep:
MO-LCAO Appr ox i mat i on

Electron positions in molecular orbitals can be
approximated by a Linear Combination of Atomic
Orbitals (LCAO).

This reduces the problem of finding the best
functional form for the molecular orbitals to the
much simpler one of optimizing a set of coefficients
(c
n

) in a linear equation:


|

= c
1

_
1

+ c
2
_

2

+ c
3

_

3

+ c
4

_

4

+

where |

is the molecular orbital (MO) wavefunction
and

_

n

represent atomic orbital (AO) wavefunctions.
27
One st ep mor e:
Basi s set s (BS)

A basis set

is a set of analytical functions (
k

) used to
represent the shapes of atomic orbitals _

n
:

General

contracted

BS: _

n

=
k
b
k(n)

k(n)

Contraction coefficients are calculated in a separate
atomic HF calculation;
if k=1 basis set is called uncontracted.

Basis sets in common use have a simple mathematical
form for representing the radial distribution of electron
density.

Most commonly used are Gaussian basis sets, which
approximate the better, but more numerically
complicated Slater-Type orbitals (STO).
28
Har t r ee-Foc k Sel f -Consi st ent
Fi el d (SCF) Met hod.
Har t r ee-Foc k Sel f -Consi st ent
Fi el d (SCF) Met hod.
Computational methodology (Jacobi iterations):
1.

Guess the orbital occupation (position) of an electron
(set of MO coefficients {c
n

})
2.

Calculate the potential each electron would experience
from all other electrons (Fock operator F ({c
n

}))
3.

Solve for Fock equations to generate a new, improved
guess at the positions of the electrons (new {c
n

})
4.

Repeat above two steps until the wavefunction for the
electrons is consistent with the field that it and the other
electrons produce (SCF).
29
Types of HF

Multiplicity (M) = 2*S+1
(S is the total spin of the system)

Electrons can have spin up or down

. Most
calculations are closed shell calculations (M=1),
using doubly occupied orbitals, holding two
electrons of opposite spins. RHF

restricted HF

Open shell systems (M>1)

are calculated by
1.

ROHF

restricted open shell HF

the same
spatial orbitals for different spin-orbitals from the
valence pair;
2.

UHF

unrestricted HF

different spatial parts for
different spins from the same valence pair
30
I l l ust r at i ng an RHF si ngl et , and
ROHF and UHF doubl et st at es
31
Semi -empi r i c al MO Cal c ul at i ons:
Fur t her Si mpl i f i c at i ons of HF
Semi -empi r i c al MO Cal c ul at i ons:
Fur t her Si mpl i f i c at i ons of HF

Neglect core (1s) electrons; replace integral for H
core

by an
empirical or calculated parameter

Neglect various other interactions between electrons on
adjacent atoms: CNDO, INDO, MINDO/3, MNDO, etc.

Add parameters so as to make the simplified calculation give
results in agreement with observables (atomic spectra or
molecular properties).
/2 /2 /2
1 1 1
1
2 (2 )
2
n n n
core
HF ii ij ij
i i j
E H J K
= = =
= +

2
1 1
1

(1) (1) (1) (1) / (1)

2
core core
ii i i i I I i
I
H H Z r | | | | = V

12 12
(1) (2)1/ (1) (2) , (1) (2)1/ (1) (2)
ij i j i j ij i j j i
J r K r | | | | | | | |
32
Beyond t he SCF.
Cor r el at ed Met hods (CM)

Include more explicit interaction of electrons than HF :
E
corr

= E -

E
HF
, where E+ = H +

Most CMs

begin with HF wavefunction, then incorporate
varying amounts of electron-electron interaction by mixing in
excited state determinants with ground state HF determinant

The limit of infinite basis set

& complete electron correlation

is
the exact solution of Schrdinger equation (which is still an
approximation)
33
Beyond t he SCF.
Cor r el at i on ef f ec t s on pr oper t i es.
34
Tw o al t er nat i ve w ays of t he
el ec t r on c or r el at i on t r eat ment
HF (Hartree-Fock)

a singe determinant

theory

no correlation included!
1. WF based multi-determinant

correlation methods:
1.

Configuration Interaction

(CI)

Variational; CISD, CSID(T)
2.

Many-body perturbation theory

(including coupled cluster)

Non-variational; MBPT2, MBPT3; CCSD; CCSD(T)
2. Density functional theory (DFT)

correlation method not based on
wave-function, but rather on modification of the energy functional:

A single determinant

theory including correlation!
/ 2 / 2 / 2
1 1 1
2 ( )
n n n
core Exch Corr
DFT i ij ij
i i j
E H J X
+
= = =
= + +

35
Summar y of Choi c es:
6-311++G**
6-311G**
6-311G*
3-21G*
3-21G
STO-3G
STO
HF CI QCISD QCISDT MP2 MP3 MP4 correlation

increasing
size of
basis set
increasing level of theory
Schrodinger
increasing accuracy,
increasing cpu time
infinite basis set
full e
-
36
The ex t r a di mensi on:
37
Summar y: Level s of QM Theor y
H=E
Born-Oppenheimer approximation
Single determinant SCF
Semi-empirical methods
Correlation approaches:
1.Multi-determinantial (MCSCF, CI, CC, MBPT)
2. Single determinantial

(DFT)
38
Some appl i c at i ons dur i ng your
w or k ...

Calculation of reaction pathways (mechanisms)

Determination of reaction intermediates and
transition structures

Visualization of orbital interactions (formation of new
bonds, breaking bonds as a reaction proceeds)

Shapes of molecules including their charge
distribution (electron density)

NMR chemical shift prediction.

IR spectra calculation and interpretation.
39
Method Type Features Advantages Disadvantages Best for
Molecular
Mechanic
-

Uses classical
physics
-

Relies on force-field
with embedded
empirical parameters
-

Computationally
least intensive - fast
and useful with
limited computer
resources
-

Good for:

Enthalpy of
Formation
(sometimes)

Dipole Moment

Geometry (bond
lengths, bond angles,
dihedral angles) of
lowest energy
conformation.
Particular force
field, applicable only
for a limited class of
molecules
Does not calculate
electronic properties
Requires
experimental data
(or data from ab

initio

calculations)
Large systems
(~1000 of atoms)
-

Can be used for
molecules as large as
enzymes
Systems or processes
with no breaking or
forming of bonds
Semi-Empirical
-

Uses quantum
physics
-

Uses experimentally
derived empirical
parameters
-

Uses many
approximations
-

Less demanding
computationally than
ab

initio

methods
-

Capable of
calculating transition
states and excited
states
-

Requires
experimental data
(or data from ab

initio) for
parameters
-

Less rigorous than
ab

initio) methods
-

Medium-sized
systems (hundreds of
atoms)
-

Systems involving
electronic transition
Ab

Initio
-

Uses quantum
physics
-

Mathematically
rigorous, no
empirical parameters
-

Uses approximation
extensively
-

Useful for a broad
range of systems
-

does not depend on
experimental data
-

Capable of
calculating transition
states and excited
states
-

Computationally
expensive
-

Small systems (tens
of atoms)
-

Systems involving
electronic transition
-

Molecules without
available
experimental data
-

Systems requiring
rigorous accuracy