Introduction to

Quantum mechanics and Molecular

Spectra
Ka-Lok Ng
Asia University

Contents
The postulates of quantum mechanics (QM)
The wave equation Schrodinger equation
Quantum mechanical operators
Eigenvalues of QM operators
Wave functions
The particle in a 1D box
Physical methods of determining the 3D structure of proteins
References
House J.E. Fundamentals of quantum chemistry, 2nd ed.
Elsevier 2004
Whitford D. Proteins: structure and function. J. Wiley 2005.
http://www.spaceandmotion.com/Physics-Erwin-Schrodinger.h
tm
Molecular spectra, see
http://spiff.rit.edu/classes/phys315/lectures/lect_14/lect_14.ht
ml
http://cref.if.ufrgs.br/hiperfisica/hbase/molecule/molec.html#c

The postulates of quantum mechanics (QM)

Postulate I
For any possible state of a system, there is a function of the coordinates of
the parts of the system and time that completely describes the system.

( x, y , z , t )
Is called a wave function. For two particles system,

( x1 , y1 , z1 , x2 , y2 , z 2 , t )
The wave function square 2 is proportional to probability. Since may be
complex, we are interested in *, where * is the complex conjugate (i -i) of
.
The quantity *dis proportional to the probability of finding the particles of the
system in the volume element, d = dxdydz.
*

d 1

all _ space

that is the probability of finding the particle in the universe is 1 normalization

condition.

The postulates of quantum mechanics (QM)

Orthogonal of two wave functions

*d 0
*d 0
Example: sin and cos are orthogonal functions.

sin cosd 0
0

Fourier series expansion sin(n) and cos(n) orthogonal functions

The Wave Equation

In 1924 de Brogile shown that a moving particle has a wave character.

This idea was demonstrated in 1927 by Davisson and Germer when an
electron beam was diffracted by a nickel crystal.
According to the de Brogile relationship, there is a wavelength
associate with a moving particle which h
is given by

mv

where, h, m and v denote the wavelength, Plancks constant, mass and velocity.
Erwin Schrodinger adapted the wave model to the problem of the hydrogen atom and
propose the Schrodinger equation. The model needs to describe a three-dimensional
wave.
Classical physics the flooded planet problem = the waveforms that would result form a
disturbance of a sphere that is covered with water
The classical 3D wave equation is

2 2 2 1 2
2 2 2 2
2
x y z v t
where is the amplitude function and v is the phase velocity of the wave.
Schrodinger equation

The Wave Equation

The Schrodinger wave equation

2 2 2 4 2 m 2 2( E V )
2 2

2
2
x y z
h
m
The 1D wave equation solution
http://www-solar.mcs.st-and.ac.uk/~alan/MT2003/PDE
/node12.html

The 2D wave equation solution

http://www.math.harvard.edu/archive/21b_fall_03/waves/index.html

Operators
Postulate II
With every physical observable q there is associated an operator Q, which
when operating upon the wavefunction associated with a definite value of
that observable will yield that value times the wavefunction , i.e. Q = q.

http://hyperphysics.phy-astr.gsu.edu/hbase/quantum/qmoper.html

Operators
(1) The operators are linear, which means that
O( ) = O + O
The linear character of the operator is related to the superposition of states
and waves reinforcing each other in the process
(2) The second property of the operators is that they are Hermitian (the 19th
century French mathematician Charles Hermite).
Hermitian matrix is defined as the transpose of the complex conjugate (*) of a
matrix is equal to itself, i.e. (M*)T = M
x iy
a

M
x

iy
c

x iy
a

M *
x

iy
c

x iy
a
M
( M * )T
x

iy
c

In QM, the operator O is Hermitian if

*
* *

C. Hermite

http://commons.wikimedia.org/wiki/Image:Charles_Hermite_circa_1887.jpg

Eigenvalues of QM operator
Postulate III
The permissible values that a dynamical variable may have
are those given by O = a, where is the eigenfunction
of the QM operator (Hermitian) O that corresponds to the
observable whose permissible real values are a.
The is postulate can be stated in the form of an equation as

O
operator

wave function

= a
eignevalue

wave function

Example Let = e2x and O=d/dx

d/dx = d(e2x)/dx = 2 e2x
is an eigenfunction of the operator d/dx with an
eigenvalue of 2.

Eigenvalues of QM operator
Eigenvalues of QM operator must be real !
Example

a
b ic

M
d
b ic
solve Mx x
(a )(d ) (b ic)(b ic) 0

2 (a d ) ad b 2 c 2 0
The two values for are real

Wave functions
Postulate IV
The state function is given as a solution of

H E

Schrodinger equation

where H is the total energy operator, that is the Hamiltonian operator.

The hamiltonian function is the total energy, T+V, where T is the kinetic energy and
V is the potential energy. In operator form

H T V
where T is the operator for kinetic energy and V is the operator for potential energy.
In differential operator form, the time dependent Schrodinger equation is

h2
2
2
2
h

V
(
q
,
t
))

(
q
,
t
)

(qi , t )
i
i
2
2
2
2
8m x
y
z
2i t
where qi is the generalized coordinates, m is the mass of the particle.

The particle in a one-dimensional box

We treat the behavior of a particle that is confined to

motion in a box
The coordinate system for this problem is show at the
right
The Hamiltonian operator, H, is H = T + V = p 2/2m + V
where p is the momentum, mass is the mass of the
particle, and V is the potential energy
Outside the box V = , so the Schrodinger equation

H E
h2 d 2

E
8m 2 dx 2

For the equation to be valid, must be 0 Boundary

condition = the probability of finding the particle
outside the box is zero
Inside the box, V = 0, so the Schrodinger equation
becomes

h2 d 2

E
2
2
8m dx

http://www.everyscience.com/Chemistry/Physical/Quantum_Mechanics/a.1128.php

The particle in a one-dimensional box

d 2
2

k
0
2
dx
Where k2 = 82mE/h2. This is a linear differential equation
with constant coefficients, which have a solution fo the
form = A cos(kx) + B sin(kx).
The constant A and B must be evaluated using the
boundary conditions. Boundary conditions are those
requirments that must be met becase of the the physical
limits fo the system.
For the probability of finding the particle to vanish at the
walls of the box, that is = 0 both at x0 and xL.
At x0
= 0 = A + B(0) A = 0
At xL
= 0 = B sin kL
Since B 0, otherwise the complete wavefunction = 0 !
sin kL = 0 that is kL = n quantization condition !

The particle in a one-dimensional box

quantization condition kL = n
Recall k2 = 82mE/h2
k2 L2 = 82mE/h2 L2 = n22, where n = 1, 2 . is the quantum number

n2h2
E
8mL2

Zero-point energy
One quantum number arise from a 1D system

E ~ n2
E ~ 1/L2
E~m
To determine the wavefunction , one uses the normalization condition
L

d B
*

all _ space

( x)

sin (n / L) xdx 1
2

n = 1, 2, 3

2
nx
sin(
)
L
L

http://www.everyscience.com/Chemistry/Physical/Quantum_Mechanics/a.1128.php

The particle in a one-dimensional box

Consider a carbon chain like
C=C-C=C-C
as an arrangement where the electrons can move along
the chain. If we take an average bond length of 1.40
Angstrom, the entire chain would be 5.60 Angstrom length,
Therefore, the energy difference between the n=1 and n=2
state would be
2
27
2

3h
3(6.63 10 erg s )

8mL2 8(9.10 10 28 g )(5.60 10 8 cm) 2

E 5.78 10 12 erg
The energy corresponds to a wavelength of 344 nm, and the maximum in the
absorption spectrum of 1,3-pentadiene is found at 224 nm. Although this not
close agreement, the simple model does predict absorption in the UV region of
the spectrum.

Molecular Spectra
Three types of energy levels in molecules
electronic: large energy separations (200-400 kJ/mol) optical or UV
vibrational: medium energy separations (10-40 kJ/mol) Infrared
rotational: small energy separations (10-40 J/mol) microwave
All the energy levels are quantized

Molecular Spectra
For a spectral line of 6000 Angstrom, which is in the visible light
region, the corresponding energy is E = hc/ = 3.3x10-12 erg
a molar quantity multiply by Avogadros number E = 200 kJ/mol
Diatmoic molecule can be viewed as if they are held together by
bonds that have some stretching and bending (vibrational)
capability, and the whole molecule can rotate as a unit.

http://cref.if.ufrgs.br/hiperfisica/hbase/molecule/molec.html#c2

Molecular Spectra
Normal mode of vibration for the CO 2
molecule
behaves much like a simple harmonic
oscillator
The vibrational energies can therefore be
described by the relation (+1/2)*h, where
, the vibrational quantum number =
0,1,2,3. and =the classical frequency
the symmetric stretch mode

the asymmetric stretch mode

the bending mode

http://www.phy.davidson.edu/StuHome/shmeidt/JuniorLab/CO2Laser/Theory.htm

Vibrational and Rotational energy levels transition spectra

The CO2 molecule is free to rotate. The energies of the rotational
modes (E = h2/(82I), where I is the moment of inertia)) are
smaller than for vibrational modes. Hence, the energy levels for
two vibrational states with the rotational divisions looks like:

Vibrational and Rotational energy levels transition spectra for HCl

http://universe-review.ca/F12-molecule.htm

Applications of the Vibrational Energy Levels

determination of bond lengths

determination of bond force constants
determination of bond dissociation energy
qualitative and quantitative chemical
analysis

Selection rules for energy level transitions

Selection rules are divided into high probability or allowed
transitions
and Forbidden transitions of much lower probability
Forbidden transition symmetry-forbidden and spin-forbidden
transitions
Spin-forbidden transitions involve a change in spin multiplicity
defined as 2S+1 where S is the electron spin number. Spin
multiplicity reflects electron pairing (see Table). For a favourable
transition there is no change in multiplicity (S=0)

Number of
unpair
electrons

Electron
spin S

2S+1 Multiplicity

Singlet

Doublet

Triplet

3/2

quartet

Selection rules for energy level transitions

Symmetry-forbidden transitions reflect redistributin of
charge during transitions in a quantity called the transition
dipole moment.
Differences in dipole moment arise from the different
electron distributions of ground and excited states
For an allowing transition it requires a change in dipole
moment
EM radiation can induce Rotational transitions only in
molecule with a permanent dipole moment.
Not all molecules have dipole moments!
(1) only polar molecules can absorb and emit electromagnetic
photons
(2) non-polar molecules : H2 ,CO2 ,CH4
(3) energy transfer can take place during collisions

The intensity of the signals in a rotational spectrum

increase with the molecular dipole moment.

Fluorescence Spectroscopy
Fluorescence excited molecules decay to
the ground state via the emission of a
photon with S = 0 ( no change in spin
multiplicity, S1 S0)
Emission is occurs at longer wavelengths
than the corresponding absorbance band
Quantum yield of Fluorescence emission
= photons emitted/number of photons
absorbed
maximum value of quantum yield is 1
Photophysical properties of a fluorophore
can be used to obtain information on its
immediate molecular environment.
Relaxation of a fluorophore from its excited
state can be accelerated by fluorescence
resonance energy transfer (FRET).
FRETcan be used to characterize proteinprotein interactions as observed in
signaling complexes of ion channel
proteins.

http://www.physiologie.uni-freiburg.de/fluorscence.html

Raman Spectroscopy

Chandrasekhara Venkata Raman (1888-1970) who discovered in 1928

that light interacts with molecules vai absorbance, transmission or
scattering
the first Indian Nobel Laureate in physics
Raman made many major scientific discoveries in acoustics, ultrasonic,
optics, magnetism and crystal physics
Scattering can occur at the same wavelength when it is known as
Rayleigh scattering (elastic, 0) or it can occur at altered frequency
(change in the colour of the scattered light) when it is the Raman effect

Figure. See http://www.search.com/reference/Raman_spectroscopy

http://www.vigyanprasar.gov.in/dream/feb2002/article1.htm

Figure. See http://www.inphotonics.com/raman.htm

Raman Spectroscopy
some weaker bands of shifted frequency are detected.
Moreover, while most of the shifted bands are of lower
frequency 0 - i, there are some at higher frequency, 0 + i.
By analogy to fluorescence spectrometry, the former are called
Stokes bands and the latter anti-Stokes bands. The Stokes and
anti-Stokes bands are equally displaced about the Rayleigh
band; however, the intensity of the anti-Stokes bands is much
weaker than the Stokes bands and they are seldom observed.

http://www.gfz-potsdam.de/pb4/pg2/equipment/raman/raman.html

Raman Spectroscopy Application

commonly used in chemistry
provides a fingerprint by which the molecule can
be identified. The fingerprint region of organic
molecules is in the range 500-2000 cm-1.
to study changes in chemical bonding, e.g. when a
substrate is added to an enzyme.
Raman gas analyzers have many practical
applications, for instance they are used in medicine
for real-time monitoring of anaesthetic ( )
and respiratory gas mixtures during surgery.
In solid state physics, spontaneous Raman
spectroscopy is used to, among other things,
characterize materials, measure temperature, and
find the crystallographic orientation of a sample.
http://www.search.com/reference/Raman_spectroscopy

Nuclear Magnetic Resonance Spectroscopy

In 1945, the NMR phenomenon was given
by F. Bloch and E. M. Purcell (both share
the 1952 Nobel Prize)
NMR spectra are observed upon the pulse
absorption of a photon (radio frequency)
of energy and the transition of nuclear
spins from ground to excited states

Bloch F (1905-1983)

Purcell E.M. (1912-1997)

http://nobelprize.org/nobel_prizes/physics/laureates/1952/
http://cancer.stanford.edu/research/milestones/
http://www.pulseblaster.com/gallery/1.html

Nuclear Magnetic Resonance Spectroscopy

For 1H there are two orientations. In one orientation the
protons are aligned with the external magnetic field (north
pole of the nucleus aligned with the south pole of the
magnet and south pole of the nucleus with the north pole of
the magnet) and in the other where the nuclei are aligned
against the field (north with north, south with south)

= aligned against
= aligned with

A spinning nucleus is
equivalent to a magnet
http://www.brynmawr.edu/Acads/Chem/mnerzsto/The_Basics_Nuclear_Magnetic_Resonance%20_Spectroscopy_2.htm
http://vam.anest.ufl.edu/simulations/nuclearmagneticresonance.php

Nuclear Magnetic Resonance Spectroscopy

Nuclei possessing angular moment (also called
spin) have an associated magnetic moment
(current generate magnetic field). Certain
atomic nuclei, such as 1H, 13C, 15N and 31P
have spin S= and 2H, 14N have spin S=1,
18O has S=5/2).
For nuclei such as 12C is the most common
isotope is NMR silent, that is not magnetic. If
a nucleus is not magnetic, it can't be studied
by nuclear magnetic resonance
spectroscopy. For the purposes, biomolecular
NMR spectroscopy requires proteins
enriched with 1H, 13C or 15N or ideally all
H 0
f
nuclei.
2
Nuclear transitions differed in frequency from
one nucleus to another but also showed
f frequency _ of _ absorption
subtle differences according to the nature of
gyromagnet ic _ ratio _ of _ the _ nucleus
the chemical group (chemical shift effect).
Methyl protons resonating at a frequency H 0 external _ magnetic _ field
amide proton -carbon proton -carbon
proton The chemical environment of such The frequency range needed to excite
nuclei are different
protons is relatively high. It ranges from
Probe by NMR and this technique can be
exploited to give information on the
300 MHz to 900 MHz.
distances between atoms in a molecules.
These distances can then be used to derive
a 3D model of the molecule.

Nuclear Magnetic Resonance Spectroscopy

Why do we see peaks ?
When the excited nuclei in the beta orientation start to relax back down to
the alpha orientation, a fluctuating magnetic field is created. This
fluctuating field generates a current in a receiver coil that is around the
sample. The current is electronically converted into a peak.
Why do we see peaks at different positions?
because nuclei that are not in identical structural situations do not
experience the external magnetic field to the same extent. The nuclei are
shielded or deshielded due to small local fields generated by circulating ,
and lone pair electrons.

NMR spectra

Solid-state 900 MHz (21.1 tesla) NMR spectrometer

at the Canadian National Ultrahigh-field NMR Facility
for Solids.
http://www.answers.com/topic/solid-state-nuclear-magnetic-resonance
http://www.scielo.br/scielo.php?pid=S0100-41582002000500017&script=sci_arttext

Nuclear Magnetic Resonance Spectroscopy

Limitations for NMR methods
1. For small proteins with size < 100 kD
2. Require highly concentrated protein solutions on
the order of 1-2 mM.
3. pH of solution < 6.