e-PG Pathshala

Subject: BIOPHYSICS

Paper 02: Quantum Biophysics

Module 01: Need for quantum theory and the Bohr model

Principal Investigator: Prof.

Moganty R. Rajeswari
Professor, Department of Biochemistry
All India Institute of Medical Sciences, New Delhi

Co-Principal Investigator: Prof. T. P. Singh

Distinguished Biotechnology Research Professor
All India Institute of Medical Sciences, New Delhi

Paper Coordinator and Content Writer: Prof. Rabi Majumdar

Emeritus Professor, Department of Natural Sciences
West Bengal University of Technology, Kolkata
Formerly Professor and Head, Biophysics Division
Saha Institute of Nuclear Physics, Kolkata

Content Reviewer: Prof. Manju Bansal

Professor, Molecular Biology Unit
Indian Institute of Science, Bangalore

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Introduction

Quantum mechanics is essential to explore the structure of atoms, molecules and nucleus, where classical
laws based on Newton’s laws of motion fail. It is important to understand the discrete energy levels in an
atom leading to the observed atomic spectra. In this module, we describe the Bohr model for circular
orbits and developments based on this model. Extension to elliptical orbits leading to shell structure of
atoms and the distribution of electrons in these shells leads to Periodic Table for elements. Why do we
call this paper Quantum Biophysics? This is because our ultimate aim is to learn all about applying
quantum mechanics to determine the structure of biologically important molecules.

Learning Outcome

● According to the Bohr model, electrons in an atom can occupy only specific circular orbits with discrete
energy levels. This is unlike a satellite, which can take up any orbit around the earth.

● Observed series of lines in different regions of the hydrogen spectrum (e.g., Balmer series in the visible
region) arise due to jumping of electronics from one energy level to another.

● Extension of the Bohr model to include elliptical orbits leads to the idea of atomic shells. All orbits in a
given shell have the same energy.

● Identification of characteristic K-lines in the x-ray region for heavy elements like molybdenum or
tungsten confirms the atomic shell structure.

● Arrangement of electrons in atomic shells , constrained by Pauli’s exclusion principle, finally leads to
Periodic Table for elements.

1.1 Need for Quantum Theory

Classical mechanics, based on Newton’s laws of motion, can predict the motion of planets around the sun
accurately. Similarly, it can also predict the motion of satellites around the earth. We know that a satellite
can be launched at any desired orbit and all such orbits are permissible. In an orbit of any given radius,
the energy of the satellite can be calculated by using the laws of classical mechanics. Thus there is no
restriction on the radius of the orbit or the energy of a satellite orbiting the earth. But the same is not true
for an electron inside the atom. Planetary model for the atom was first proposed by Rutherford on the
basis of a famous experiment, where atoms were bombarded with alpha particles. Although the electrons
are similar to planets or satellites in a much smaller system like the atom, things are quite different there.
In any atom, an electron can only occupy a set of permissible or allowed orbits around the atomic nucleus
and has discrete energy levels. Laws of classical mechanics fail to predict this discreteness. Quantum
theory, on the other hand, helps us to identify these allowed orbits for the electrons and calculate their
energy levels. In the Bohr model for atoms, these are called the electronic energy levels in an atom or
simply the atomic energy levels.

Electrons absorb or emit light of a specific wavelength in jumping from one orbit into another. Let the
electronic transition occur from an orbit of a lower energy level E1 to that of a higher energy level E2 . The
energy gap E between the two orbits is (E2 – E1 ) and the absorbed wavelength  is obtained from the
relation

E = h = hc/ (1.1)

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where h = 6.6 x 10-34 J.s is the famous Planck’s constant. The missing wavelength  gives a dark line in
the hydrogen spectrum. Several series of such dark lines are detected in the absorption spectrum of
hydrogen atom. One of these, the Balmer Series, is easier to detect as it shows up in the visible region of
the spectrum, while the others appear in the UV (ultraviolet) and IR (infrared) regions. All the dark lines
or the missing wavelengths are due to electronic transitions, which strongly indicate the presence of
discrete energy levels in the atom. These energy levels were calculated, for the first time, on the basis of
the Bohr model for atoms.

1.2 Why Quantum Biophysics?

Before passing on to the Bohr Model, we must be clear about the role of Quantum Mechanics in
Biophysics. After discovery of the DNA double helix structure (Watson-Crick model), the key role of
Modern Biology is to identify the structural aspects of proteins and other molecules that regulate the gene
and keep our cells alive. In this way, once the basic problem in biology reduces to the study of molecular
structures, Biophysics starts playing a major role. In long chain molecules, for example, their folding
pattern depends on how the electron charges are distributed in the molecule. This involves Quantum
Mechanics.

Though the Bohr model is a great leap forward, but it must be kept in mind that this model is the basis of
old quantum theory, which cannot take us much beyond the atomic structure. It has been successful in
obtaining the discrete energy levels of electrons in atoms and could also account for the distribution of
these electrons in atomic orbits and shells, leading to periodic classification of elements. However, it
could not predict the behavior of electrons in molecules. Biophysics and modern structural biology
involves the study of chemical bonds as well as the electronic and other transitions involving vibrations,
rotations, and folding in molecules. For these, we need to solve the Schrodinger wave equation, which
forms the basis of modern quantum theory. Quantum Biophysics is thus an essential component of our
PG Pathshala course.

Fig. 1.1 Hydrogen Atom

1.3 The Bohr Model

The Bohr model was first applied to hydrogen atom. It is valid for circular orbits though it was later
extended to include elliptic orbits as well.

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Bohr postulated that the only allowed orbits for electron in an atom are those, for which the angular
momentum L of an electron is an integral multiple of  = h/2 , where h denotes the Planck’s constant.
An electron of mass m moving with speed v along a circle of radius r around the atomic nucleus has
magnitudes of linear momentum p = mv and angular momentum L = rp = mvr (see Fig. 1.1). Therefore,
according to Bohr’s postulate, the radius r of the allowed orbits must satisfy the quantum condition:

nh
mr   n (1.2)
2
or
n
p (1.3)
r
In this equation, n is a positive integer. We combine this condition with the usual classical equation of
motion of the electron, obtained by equating the centripetal force to the electrostatic force of attraction
due to the nucleus:

m 2 Ze 2
k 2 (1.4)
r r
or
p2 Ze 2
k (1.5)
2m 2r

In this equation, the electronic charge e = 1.6 x 10-19 C, and the Coulomb constant k = (1/40 ) = 8.99 x
109 N.m2 /C2 , where the permeability of free space  0 = 8.85 x 10-12 C2 /(N.m2 ). The atomic number Z = 1
for a hydrogen atom, where the nucleus contains a single proton only.

Eliminating p from the equations (1.3) and (1.5), the allowed radii are

n2 2
r  rn  2
 n2a (1.6)
kZme
The positive integer n is called the quantum number. The ground state of the hydrogen atom has n = 1.
So the radius of the ground state electron is

2
a  r1  (1.7)
kme2
This is called the Bohr radius. The total energy of the electron can be expressed as a sum of the kinetic
and potential energies. Thus the total energy is given by the energy-momentum equation

1 p2
E m 2  V (r )   V (r ) (1.8)
2 2m
For a free particle, V = 0, but in this case, the electron is under an attractive Coulomb potential. So the
potential energy has the form

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 Ze 2
V (r )  k (1.9)
r

Using equations (1.5) and (1.9) for kinetic and potential energies, the equation (1.8) for total energy of the
electron becomes

Ze 2
E  k (1.10)
2r

Plugging in the allowed values of the radius r from equation (1.7), the discrete energy levels of the
electron are given by

k 2 Z 2 me 4 2 2 k 2 Z 2 me 4
E  En    (1.11)
2n 2  2 n2h2

It is important to note that En  1/n 2 . It should also be realized that an electron, moving with uniform
speed in a circular orbit, is accelerated towards the centre of the circle.

NEILS BOHR

According to classical theory of radiation, an accelerated electron radiates light and loses energy
spontaneously (e.g., see, Fig. 1.2, where x-rays are emitted by energetic electrons impinging on a metal
target). Bohr postulated that this does not happen for electrons in orbits that satisfy the condition (1.2), as
otherwise an atom would not be stable as we see it. So the allowed orbits in atoms are radiationless, but
light is emitted or absorbed when an electron changes its orbit and jumps from one orbit to another.

1.4 Atomic Energy Levels: A Working Formula

The MKS units for length and energy, namely metre (m) and Joule (J), are too large to describe the world
of atoms and molecules. The practical unit of length in such cases is a nanometer (nm) or an angstrom

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(Å), while the practical unit of energy is an electron-volt (eV). The conversion factors are 1 nm = 10-9 m, 1
Å = 10-10 m = 0.1 nm, and 1 eV = 1.6 x 10-19 J.

The ground state energy E1 of an atom is obtained by putting n = 1 in equation (1.10). For a hydrogen
atom (Z =1), it may be checked that E1 = -13.6 eV. As a result, the equation (1.10) turns into a useful
working formula

E1 Z 2 13.6Z 2
En    eV (1.12)
n2 n2
The energy required to knock out the ground state electron of an atom is its ionization energy. Thus, for
hydrogen atom, it is - E1 = 13.6 eV.

The effective atomic number Z for an atom other than hydrogen is always less than the number of
protons. The reason is that for an atom with many electrons, the positively charged nucleus is shielded by
electrons in the inner orbits. As a result, an outer electron (such as the outermost electron of sodium) feels
the effect of a reduced nuclear charge. In such cases, mutual repulsion of the electrons also perturbs the
energy levels.

When an electron jumps from one level to another in an atom, it absorbs or emits a specific wavelength
of light  given by E = h = hc/. This wavelength appears as a dark line in the atomic absorption
spectrum or a bright line in the emission spectrum. The spectrum of hydrogen atoms in hot stars was
found to have a series of such lines. The only series in the visible region is called the Balmer series. All
other series are in ultraviolet (UV) or infrared (IR) regions.

1.5 Balmer Series and the Hydrogen Spectrum

In 1885, a Swiss school-teacher Balmer discovered a series of dark lines in the visible region of the
absorption spectrum of hydrogen. This indicated a series of missing wavelengths in the spectrum. It was
found that these wavelengths could be produced successfully from the empirical formula

1  1 1 
 R 2  2  (1.13)
 2 n 

where R = 1.097 x 107 m-1 is called the Rydberg constant, and n =3, 4, 5, 6, and so on. There was no
knowledge of the atomic structure in those days. Therefore, the formula was discovered by using trial-
and-error methods only.

Using equation (1.10) for the energy levels obtained from the Bohr model, the wavelength of light
absorbed by an electron in jumping from an initial orbit n i to a final orbit n f can be calculated by from the
relation E = (Ef – Ei) = h = hc/, where E is the energy gap between the two orbits. Thus the
wavelengths appearing as missing lines in the absorption spectrum are give by

1 E 2 2 k 2 Z 2 me 4  1 1  
2 1 1 
     RZ  (1.14)
 hc h 3c n 2 n 2  n 2 n 2 
 i f   i f 
where
R = (2 2k2 me4 /h 3c) = 1.097 x 107 m-1 (1.15)

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is the Rydberg constant. This is in perfect agreement with the value predicted by Balmer. Moreover, for
hydrogen atom (Z = 1), this formula with n i = 2 and n f = 3, 4, 5, 6, etc. becomes identical to the simple
empirical formula used by Balmer to calculate the wavelengths of missing lines in visible region of the
absorption spectrum. This proves the correctness of the Bohr model.

It follows that the missing wavelengths in Balmer series occur as the electrons absorb light when they
jump from the first excited level (n = 2) of the hydrogen atom to higher levels. Missing wavelengths
appear as bright lines in the emission spectrum as the electrons emit light when they fall back to the
original level (n = 2) from higher energy levels (see Fig. 1.2). The red line at 656 nm for n = 3 →2
transition is called the H alpha line. Only Balmer series is observed in the visible range, while the others
lie outside this range. In Lyman series, for example, the transitions of electrons are from higher levels to
the ground state level (n = 1) of the atom, for which the resulting wavelengths are in the UV region.
Paschen series involves transitions from higher levels to the level (n = 3) and occurs in the IR region.

Fig. 1.2 Electron transitions and emission spectrum in Balmer series.

Red line at 656 nm for n = 3 →2 transition is the H alpha line.

1.6 Elliptic Orbits and Additional Quantum Numbers

An atom is actually a three-dimensional spherical object with the electrons having circular and elliptical
orbits of different sizes. In addition, the elliptical orbits have different orientations in space. In an
elliptical orbit, the atomic nucleus is at one focus of the ellipse. A circle is a special case of ellipse with
zero eccentricity. Theory of elliptical orbits was developed by Sommerfeld. Here we will only outline the
results of this theory. In three dimensions, it is natural that an orbit should be described by three quantum
numbers n, l, and m, where n is called the principal quantum number, l is the azimuthal quantum
number, and m is the magnetic quantum number.

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The principal quantum number n is a positive integer, which defines a shell consisting of several orbits.
For example,

n = 1, 2, 3, …..

which define the K, L, M shells, and so on for an atom. For a given value of n, the azimuthal quantum
number l can assume the values

l = 0, 1, 2,…, (n – 1)

which define the s, p, d orbits, and so on. The s orbits are circular orbits, while the others are elliptical
with different sizes and orientations. For a given value of l, the magnetic quantum number m can assume
(2l + 1) values, namely

m = -l,…,0,…,+l

These results follow rigorously from solutions of the Schrodinger equation. Considering the above
values and restrictions on the set of quantum numbers nlm, we note that the K-shell (n = 1) consists of a
single circular orbit with nlm = 100 only. This is designated as the 1s orbit.

The L-shell (n = 2) consists of four orbits, namely nlm = 200, 211, 210, 21-1. The 200 orbit is designated
as the 2s orbit, while the other three orbits (211, 210, 21-1) are referred to as the 2p orbits. Out of these,
the 2s orbit is a circular orbit, while the three 2p orbits are elliptical orbits that are oriented along
different mutually perpendicular directions (2p x, 2p y, 2pz ).

In this model, some transitions from one orbit to the other are not allowed. For example, the selection
rule l =  1 forbids transition of an electron from the 2s orbit (nlm = 200) to the 1s orbit (nlm = 100) in
an atom. For this transition, l = 0, which does not meet the criterion l =  1. The 2s orbit is a
metastable state, which is important for designing lasers.

Atomic Number Element Electronic

Configuration
1 Hydrogen (H) 1s1
2 Helium (He) 1s2
3 Lithium (Li) 1s2 2s1
4 Beryllium (Be) 1s2 2s2
5 Boron (B) 1s2 2s2 2p1
6 Carbon (C) 1s2 2s2 2p 2
7 Nitrogen (N) 1s2 2s2 2p 3
8 Oxygen (O) 1s2 2s2 2p 4
9 Fluorine (F) 1s2 2s2 2p 5
10 Neon (Ne) 1s2 2s2 2p 6

Table1.1. Electronic Configurations of the first ten elements in Periodic Table.

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It can be shown that the number of orbits in a given shell with principal quantum number n is n 2. In
accordance with Pauli’s exclusion principle, each orbit can accommodate only two electrons with
opposite spins. Thus the maximum number of electrons in the shell is 2n2 . For example, the M shell with
n = 3 has 9 orbits (one 3s orbit, three 3p orbits and five 3d orbits) and can accommodate 18 electrons. The
next higher shell with n = 4 has 16 orbits (one 4s, three 4p, five 4d, and seven 4f orbits) and can
accommodate 32 electrons, and so on.

Electronic configuration of an atom tells us how the electrons are distributed in various orbits of the
atom. For example, a hydrogen atom has only one electron in a circular 1s orbit. So its electronic
configuration will be abbreviated as 1s1 . Electronic configurations of the elements from hydrogen (H) to
neon (Ne) involve K and L shells only. These are shown in Table 1.1. Arrangement of electrons in carbon
atom is shown in Fig. 1.3. All the elements found in nature are listed in the Periodic Table by filling up
the successive shells in order of ascending energy levels, but with some restrictions.

Fig. 1.3 Arrangement of electrons in carbon atom

It is important to note that for energy levels, the equation (1.10) for circular orbits still remains valid. This
is because the energy levels depend on principal quantum number n only (as in the Bohr model for
circular orbits). This explains why the Bohr model could successfully account for the hydrogen spectrum.

In the present model, there are generally more than one orbit having the same energy level. For example,
in L shell (n = 2), all four orbits (2s, 2p x, 2p y, 2p z ) have the same energy level. In such cases, we say that
there are degenerate states. It follows that for a given value of n, there is n2 -fold degeneracy.

1.17 Characteristic X-rays caused by Electron Transition

Soon after X-rays were discovered by Roentgen over a century ago, they were used for medical diagnosis.
It is well known in classical physics that an accelerated electric charge gives off radiation. This principle
is used in an x-ray tube, where the energetic electrons produced by high voltage across the tube (usually
50-100 kV) are brought to rest by letting them impinge on a heavy metal target (Fig. 1.4). This causes a
rapid deceleration or braking of the electrons, as a result of which the high energy x-rays are emitted
These x-rays cover a wide range of wavelengths mostly below 0.1 nm (much shorter than the UV
wavelengths), producing the continuous part of the spectrum (Fig. 1.5). Value of the cut-off wavelength
min depends on the tube voltage V and can be determined by using the relation eV = hc/

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If the target happens to be an element with large atomic number, such as molybdenum (Z = 42) or
tungsten (Z = 74), there are also sharp emission peaks superimposed on the continuous spectrum. The
peaks for molybdenum are shown in Fig. 1.5. Wavelengths of these peaks are characteristic of the target
material only. So these are called characteristic x-rays. The peaks appear as some of the incident
electrons are energetic enough to knock out K shell electrons from the target atom in x-ray tube. As a
result, the vacancies created in the K shell are filled up by outer shell electrons, which fall back into the K
shell, emitting photons.

Fig. 1.4 Energetic electrons produce X-rays while decelerated by impinging on a heavy metal target.

Fig. 1.5 The K and K lines characteristic of molybdenum.

For an element like molybdenum having large atomic number (Z = 42), the photons emitted are high
energy x-ray photons. This is because the Rydberg equation (1.14) tells us that larger values of Z lead to

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shorter wavelengths. When an electron drops from the n = 2 level to the K shell, the resulting x-ray peak
is called the K line. Similarly, when an electron drops from a higher level n = 3 to the K shell, we get the
K line, which is less intense and appears at a shorter wavelength. These K and K lines help us to
conclude that the atomic energy levels are discrete as described by the Bohr model.

Summary

● The Bohr model gives discrete circular orbits and energy levels of electrons in atoms.

● Observed hydrogen spectrum is due to electronic transition from one level to another.

● Extension to include elliptical orbits gives the idea of degenerate energy levels and shells.

● Characteristic K-lines for heavy elements in x-ray region confirms shell structure.

● Arrangement of electrons in atomic shells leads to Periodic Table for elements.

Thank you!

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