CHM695

March 11

Connection to frequency:
2
E
2
l6
vibrational
mode

=k

1
ni =
2p

Imaginary freq:

3N-5 vibrational
modes if planar

2
E

li2

ki

3N-6 vibrational
modes if non-planar

<0

if molecule is not having a stable structure; motion along li will

decrease energy.

Frequency Calculation Using Gaussian: H2 example

%Chk=h2.chk
#P HF/3-21G Freq Opt=Tight
Frequency Calculation of H2
0 1
H
H 1
hh

keyword to
do freq.
calculation

optimize the
structure

hh
0.8

visualize vibrations using molden:

http://www.cmbi.ru.nl/molden/vibration.html
visualize normal modes using gaussview:
http://www.gaussian.com/g_tech/gv5ref/results.htm

TS
D

For TS, frequency is complex along the reaction coordinate.

Along the all other modes, freq. is real

Vibrational freq.
Quadratic approximation:
x

f(x)

f ( x ) = f ( x0 ) +
3
1 d f
+
(
x
6 dx3 x0

df
dx

x0

x0 )3

(x

1
x0 ) +
2

d2 f
dx2

x0

(x

x0 )

a number

zero

f ( x ) = f ( x0 ) +
3
1 d f
+
(
x
6 dx3 x0

3N 3N

1
E
2 i j
qi =

mi qi

df
dx

x0 )3

2
E

qi q j
0
qi

x0

(x

1
x0 ) +
2

d2 f
dx2

x0

(x

x0 )

higher terms are ignored

qi q j
0

1
=
2

3N 6

2 E
2
li

2
li
0

ki
1 p
ni =
ki
2p

k is mass
weighted

Application of Vibrational
Analysis

frequency
from vib. analysis

qvib

exp( bhn/2)
=
1 exp( bhn)

from vib. partition function => vibrational contributions to

thermodynamic properties
Comparison to IR/Raman spectrum
There are models to incorporate anharmonicity

Planar Ammonia at HF/STO-3G level:

Compute the frequencies, and characterise the normal
modes and their frequencies.
Explain why one of the normal modes have imaginary
frequency.
What does motion along the normal mode indicate?
Hint: create an z-matrix for planar
ammonia.
Use z-matrix input and optimize the
structure of planar ammonia. By
specifying the value of an internal
coordinate within the z-mat will
constrain the structure to that value.
You may fix angles (120deg.) and
torsions (180 deg.) during
optimisation.

N
120
dNH

dNH
120

N
120

dNH

torsion H-N-H-H=180 deg.

Structure Optimization
E

qn

q0

q2

q1

1
2
E ( q ) = k ( q q0 )
2
1
2
E ( q n ) = k ( q n q0 )
2

dE
= k ( q n q0 )
dq q=qn

1 dE
q0 = q n
k dq q=qn
gradient (as arrows in the left figure)
has the direction of greatest rate of increase of E

q0 = q n

q0

q n +1 = q n

qn

dE
dq

dE
dq

q=qn

But, k is not known!

1
k

q=qn

scaling
parameter
Steepest descent method
(line search)

q0

qn q

quadratic
E

q n +1 = q n
q0

d2 E
dq2

1
q=qn

qn q
quadratic assumption

q n +1 = q n

2
d E

dq2

1
q=qn

dE
dq

q
q=qn

dE
dq

q=qn

In multi-dimensions:

q n +1 = q n
Newton-Raphson

cHn gn
Hessian

gradient

Hessian computation: usually numerical but is

computationally expensive!
BFGS Method (Quasi-Newton methods): Here H is
not computed explicitly!
Make an initial guess of H
Keeps on improving this by appropriate update
based on gradients.
Based on the change in energy, one can on-the-fly compute
appropriate c
BFGS is also usually done together with line-search method to
improve the efficiency

q
Local minima and global minima on PES can occur like above.
Standard optimizations algorithms find the local minimum,
which may not be the true global minimum. Thus different
starting structures may be experimented.

Optimizing the TS
max.

min.
normal mode with
imaginary freq.

q n +1 = q n

2
d E

dq2

1
q=qn

dE
dq

q=qn

%chk=job.chk
#hf/3-21G opt=(ts,CalcFc,Z-matrix) freq
TS OPT
-1 1
c
h 1 hc
h 1 hc
h 1 hc
cl 1 clc
cl 1 clc
hc
clc

2
3
2
2

1.089000
2.000000

120.0
120.0
90.0
90.0

2 180.0
4 90.0
3 90.0