Ashvin B. Padhiyar / Ph. D. Thesis (Physics) / Sardar Patel University - 2010
246
Chapter 8
Infrared spectra of iodine complexes with
five amino acids
Ashvin B. Padhiyar / Ph. D. Thesis (Physics) / Sardar Patel University - 2010
247
1 INTRODUCTION
Organic charge transfer complexes have been known from a
long time many of which are found to be organic semiconductors
[1-3]. Some of them are found to be low-dimensional conductors
according to anisotropic electrical and optical properties [4,5].
Charge transfer interactions among biomolecules do exist [6] but
mostly homomolecular biomolecules have been studied [7].
However, initial studies of charge transfer interactions are also
carried out among amino acids and acceptors, purine and
riboflavin, purine and pyrimidine complexes with various
acceptors and some protein complexes [8-18]. Recently we have
established two-dimensional conducting systems which are
charge transfer complexes of four amino acids namely
asparagine, arginine, glutamine and histidine on the basis of
solid state infrared spectroscopy [19]. Some other charge transfer
complexes of macromolecular biomolecules have shown hopping
of small polarons induced by charge transfer interactions at the
chain-ends of macromolecules [20].
In the present study, we report iodine complexes of five
amino acids namely asparagine, arginine, glutamine, histidine
and tryptophan as studied with IR spectroscopy. The first four
are classified as having positively charged side chains and
tryptophan is the one having non-polar group as side-chain.
2 EXPERIMENTAL PROCEDURE
The five amino acids were obtained as analytical reagent
grades from sigma chemical company, USA. Resublimed iodine
used was also pure and in crystalline form. The amino acids were
mixed one by one with iodine in an agate mortar in 1:1
Ashvin B. Padhiyar / Ph. D. Thesis (Physics) / Sardar Patel University - 2010
248
molecular weight proportions and ground with a pastle till the
characteristic colours of the charge transfer complexes were
obtained. These CT complexes were reground with dry
spectrograde KBr powder (95%) to form homogeneous and finely
dispersd powders. These mixtures were manually compressed in a
die to form circular pellets which were weakly aborbing, mainly
transmitting and negligibly reflecting.
The spectra in the full IR range (400-4000cm-1) were recorded
using a GXFTIR single beam spectrometers manufactured by
Perkin-Elmer Company, USA. It is having a resolution of
0.15cm-1, a scan range of 15,000-30-1, a scan time 20 scan per
second, and OPD velocity of 0.20cm/sec and MIRTGS and
FIRTGS detectors. A beam splitter of opt KBr type was used
having a range of 7800-371cm-1.The spectra were recorded in
purge mode.
3 RESULTS AND DISCUSSION
The FTIR (Fourier-transformed infrared spectra) spectra of
the five amino acids namely asparagine, arginine, glutamine,
histidine and tryptophan were obtained and are shown below
(Figure 1).
Thus there are three broad envelopes in absorption (100-T)
formed by constitutive independent vibrational or rotational
levels. The envelopes are due to either symmetric groups and
side chains of amino acids. The formation of envelopes is
equivalent to the formation of wave-packets of longitudinal and
transverse optical phonons associated with intramolecular
vibrations.
Ashvin B. Padhiyar / Ph. D. Thesis (Physics) / Sardar Patel University - 2010
249
Wavenumbers (cm- 1)
Figure 1 Infrared spectra of
(a) Asparagines (b) Arginine (c) Glutamine
(d) Histidine and (e) Tryptophan
Figure 2(a)
Ashvin B. Padhiyar / Ph. D. Thesis (Physics) / Sardar Patel University - 2010
250
When charge transfer complexes are formed with iodine, the
charge densities of the amino acids are altered due to charge
transfer and even the intramolecular vibrations also show
changes in amplitudes and widths of the levels due to charge
transfer interactions at various sites. There is a multi-centered
charge transfer contact. The FTIR spectrum of aspargagine-
iodine complex is shown (Figure 2a) and nature of transition is
analyzed (Figure 2b).
Ahν vs hν is found to
be a straight line showing a
forbidden direct or an
allowed indirect transition
in a two-dimensional
system. The absorption
functions as a function of
photon energy for different
dimensionality are known
(Table I) Thus asparagines-
iodine is a layered
conductor.
Figure 2 (a) IR Spectrum of asparagine - iodine (1:1) complex
(b) Ahν vs hν showing interband transition
The set of levels in the region 2000-4000 cm-1 are blue
shifted due to anharmonic interactions in asparagine-iodine.
However, the oscillator strength which is proportional to area
under the band remains almost invariant. The anharmonic
interaction is related to stretching of bonds beyond elastic limit
Ashvin B. Padhiyar / Ph. D. Thesis (Physics) / Sardar Patel University - 2010
251
and this leads to an increase in the amplitude of vibration.
Because area under the band remains invariant, the width of each
level decreases leading to the reduction of width of the envelope
formed by large number of such levels. The increase in amplitude
beyond elastic limit menifests itself as blue shift in frequency
because in a quantum mechanical picture amplitude and
frequency are proportional due to quantization of lattice
vibrations [21].
The set of levels in the region 1000-2000 cm-1 form a
Gaussian envelope which has been fitted (Figure 2c).
Figure 2 (c) Analysis of Gaussian background profile in mid-IR range
There is reduction in frequencies of levels (red-shifts) due
to scattering of deformation vibrations because of the coupling
with electronic motions in this range. Red-shifts are associated
with increase in widths of vibrational levels to keep oscillator
strength invariant. Large polarons are formed and band motion of
such polarons lead to the formation of Gaussian envelope.
Gaussian distribution reveals free charge carriers and here charge
carriers are large polarons. Polarons are electrons or holes
surrounded by virtual phonon cloud. Polaron formation is a
consequence of electron-phonon interaction usually dominant in
ionic materials rather than covalently bonded materials. The
Ashvin B. Padhiyar / Ph. D. Thesis (Physics) / Sardar Patel University - 2010
252
electron-phonon coupling constant is given by ,
where is the longitudinal optical phonon frequency. As
decreases, signifying number of virtual phonons surrounding
a charge carrier or electron-phonon coupling constant increases.
Thus width of the envelope increases as the width of the
envelope is a measure of electron-phonon coupling potential.
Gaussian background reveals band motion of polarons in two
dimensions. In one-dimension, polarons hop being constrained to
one dimension and lead to beta density as envelope as found in α-
keratin [22] and in two dimensions, polarons show band motion
as found in a planar protein called elastin [23]. Gaussian
distributions are found in charge transfer complexes of
tetramenthylbenzidine,[24], triethylamine (DDQ)2, DPPD(DDQ)2
where DPPD=N,N’-diphenyl-p-phenylene diamine and
DDQ=2,3,-dichloro-5-6-dicyano-p-benzo-quinone[25] and charge
transfer complexes of indole [26]. These are the cases where
donor molecule is highly polarizable. Thus Gaussian envelope is
directly related with the high polarizability of asparagine
molecule due to highly polar aliphatic side chain. Red-shift of
entire set of vibrational levels are due to high polarizability
determined by strongly polar bonds.
The set of levels in the region 400-1000 cm-1 show blue
shift due to anharmonic interactions as dominant mechanism.
There is reduction in width of each level contributing to
reduction in width of entire envelope associated with reduction in
coupling constant. Increase in the frequency of longitudinal
optical phonon leads to decrease in electron-phonon coupling
constant. When there is blue shift, the phonons are not easily
excited and when there is red-shift phonons are easily excited.
Ashvin B. Padhiyar / Ph. D. Thesis (Physics) / Sardar Patel University - 2010
253
Excited phonons couple with charge carriers to from polarons.
Next is the spectrum of histidine-iodine (1:1) complex
which is shown here (Figure 3a).
Figure 3 (a) IR spectrum of histidine-iodine (1:1) complex
The region 2000-4000cm-1 contains a broad envelope with
reduction in width as compared to envelope in the spectrum of
hisitdine alone. Then there is flattening in transmission between
1800 cm-1 and 3200 cm-1 corresponding to constant absorption
coefficient. This is associated with allowed direct transition in
two dimensions in a polycrystalline material. Thus histidine-
iodine is also a layered semiconductor. In the second region
between 1100 cm-1 and 1800 cm-1, there is a Gaussian envelope
with increase in width. This is the region in which the set of
vibrational levels is red-shifted. The vibrational levels are
mainly consisted of ring stretching vibrations of histidine ring.
The ring stretching vibrations in aromatic or heterocyclic side
chains lie at lower frequency as compared with bond stretching
vibrations in aliphatic side chains. Thus the ring stretching
vibrations lie in the range of deformation vibrations along
aliphatic side chains. This is due to the coupling of strongly
delocalized π-electron cloud with ring vibrations. The last region
400-1000cm-1 contains again a Gaussian envelope which is weak
and very broad again revealing band motion of polarons. This
Gaussian has reduced width and set of constituent levels is
Ashvin B. Padhiyar / Ph. D. Thesis (Physics) / Sardar Patel University - 2010
254
blue shifted. Thus histidine-I2 contain two Gaussian background
envelops which are fitted by plotting ln A vs (K-K0)2 (Figures 3b
and 3c).
Figure 3 (b) Analysis of gaussian back ground profile in high frequency range
Figure 3 (c) Analysis of gaussian background profile in low frequency range Tryptophan-iodine (1:1) complex also reveals three
background envelop in the entire range (Figure 4a).
Figure 4 (a) IR Spectrum of tryptophan-iodine (1:1) complex The stretching vibrations are blue-shifted due to anharmonic
interactions dominating and the background profile shows
Ashvin B. Padhiyar / Ph. D. Thesis (Physics) / Sardar Patel University - 2010
255
reduction in width. Nature of transition when analyzed reveals
that Ahν vs hν as rectilinear plot (Figure 4b).
Figure 4(b) Ahν vs hν showing interband transition
Figure 4 (c) Analysis of Gaussian background profi le in the
mid IR- range
This is associated with forbidden direct or allowed indirect
transition in a disordered material in two dimensions. The
analysis reveals a layered nature of tryptophan-iodine complex.
The ring vibrations reveal red-shifting associated with softening
of these optical phonons and this is associated with an increase
in width of a Gaussian background which has been fitted (Figure
4c). The Gaussian lies between 900 cm-1 and 1800 cm-1. The
Ashvin B. Padhiyar / Ph. D. Thesis (Physics) / Sardar Patel University - 2010
256
tryptophan is an amino acid with non-polar side chain containing
a heterocyclic group. The non-polar side chain leads to neutral
character of tryptophan molecule. Tryptophan is a donor
molecule due to tryptophan ring system in side chain. There are
random orientations of tryptophan molecules in solid state due to
inert nature. This leads to isotropic disorder in tryptophan and its
iodine complex. The isotropic disorder related with equal
probability for all orientations reveals itself as a semicircular
distribution in absorption vs wavenumber graphs, i.e. in
absorption spectrum. A semicircular distribution is indeed
observed in the range 500-900 cm-1. An anisotropic disorder
leads to U-shaped distribution in biocytin complexes [27]. The
last region between 400 and 600 cm-1 contains a small envelope
which has reduced width with blue shifted levels of rocking,
wagging and group vibrations.
Next is the spectrum of arginine-Iodine complex
(Figure 5a).
Figure 5 (a) IR Spectrum of arginine-iodine (1:1) complex This spectrum consists of three regions of stretching
vibrations and lowest wavenumber region of rocking, wagging
and group vibrations contain envelopes which are red-shifted due
to softening of these modes. The intermediate frequency range
contains blue-shifted envelope with reduction in electron-
Ashvin B. Padhiyar / Ph. D. Thesis (Physics) / Sardar Patel University - 2010
257
phonon coupling constant. The envelope is a Gaussian in the
intermediate range corresponding to the band motion of large
polarons in two-dimensions (Figure 5b).
Figure 5 (b) Analysis of Gaussian background profile in the mid IR-range
Again there is a flattening of transmission with constant
absorption coefficient associated with direct allowed transition in
two-dimensions. The inverted behavior of blue and red shifts as
compared to earlier three cases is related with the symmetry of
the potential related with charge transfer from I2 molecules. Thus
there are two types of iodine complexes of amino acids: Two
extreme bands blue-shifted and two extreme bands red-shifted.
Also there is observation of noise in tryptophan-iodine and
arginine-iodine complexes both in highest wavenumber region
above 3400cm-1 and in the band gap region around 1700 cm-1.
This may be related with photoconducting nature of these
complexes and localization near the band edges.
The last is the spectrum of glutamine-iodine complex
(Figure 6a).
Ashvin B. Padhiyar / Ph. D. Thesis (Physics) / Sardar Patel University - 2010
258
Figure 6 (a) IR Spectrum of glutamine-iodine (1:1) complex This also belongs to second type and spectrum is similar to
arginine-iodine complex. The two extreme envelopes are red-
shifted and the central envelope is blue-shifted. The central
background envelope and the lowest wavenumber envelope are
both small Gaussian bands associated with band motion of
polarons in two-dimensions. (Figure 6b and 6c).
Figure 6 (b) Analysis of gaussian background profile in mid-IR range
Figure 6 (c) Analysis of gaussian background profile in low-frequency range
Ashvin B. Padhiyar / Ph. D. Thesis (Physics) / Sardar Patel University - 2010
259
The two dimensional nature is again verified with analysis of
nature of transitions. The absorption Ahν vs hν is found to have
rectilinear behavior indicating allowed direct transition in two
dimensions for a polycrystalline material (Figure 6d).
Figure 6 (d) Ahν vs hν showing inter band transition The nature of transitions are summarized for all five iodine
complexes of amino acids (Table II). All the Gaussian
distributions contain three parameters namely, central frequency,
maximum absorption and full-width at half-maximum (FWHM).
These parameters are tabulated (Table-III).
The electron-phonon coupling constant is also given by
Where is the average matrix element of
electron-phonon coupling, is the density of
states at the Fermi level and is average phonon frequency. The
density of states at the Fermi level is given by N( )=
where n=d-1 and d is the dimensionality of the electron system.
For layered materials d=2 and N( ) varies linearly with . Near
the Fermi level, N( ) is very small and this reduces electron-
phonon coupling constant . In a Peierls transition or Kohn
anomaly, a band gap or pseudo-gap opens at the Fermi level
which drastically lowers the density of states at Fermi level. This
Ashvin B. Padhiyar / Ph. D. Thesis (Physics) / Sardar Patel University - 2010
260
reduces electron-phonon coupling constant ( and since the mass
of a polarons is given by 1
(1 )6polm m . The effective mass of
polaron reduces. Since the electrical conductivity is given
by2
pol
ne
m , the conductivity increases. The large polarons move
fast showing a band motion. This is related with increase in
conductivity due to softening of phonons just above the Peierls
transition temperature observed in many one-dimensional
conductors. The velocity of a polarons is given by
where is the unperturbed velocity.
In the present study two iodine complexes namely histidine-
iodine and arginine-iodine show constant absorption just above
the band gap. This can be understood using a scaling hypothesis
leading to lnlim 2
lng
d gd
d l , where g is the dimensionless
conductance, is a characteristic length and d is the
dimensionality of the electron system. This relation can be easily
extended toln
lim 2ln
dd
d
, 1 1;
4
cn n
is real part of refractive
index, where is normalized absorption coefficient, λ is
wavelength of radiation and d is the dimensionality. For two-
dimensional system (d-2), lnα vs lnλ is horizontal line with slope
zero in the large absorption region. The above relation between
electrical conductivity and absorption coefficient. ( 1 1;4
cn n
is
being real part of refractive index). is the wavelength in the
medium depending on dispersion governed by refractive index as
a function of incident wavelength. Thus scaling hypothesis
explains constant absorption in two dimensional (layered)
materials.
Ashvin B. Padhiyar / Ph. D. Thesis (Physics) / Sardar Patel University - 2010
261
The electronic conductivity vs temperature also shows a
flattening at low temperature which can be also explained with
either correlated hopping or excitonic reduction of band gap
apart from scaling hypothesis. Thus the constant absorption near
the band gap can also be explained with correlated hopping or
excitonic reduction of the band gap down to zero.
4 CONCLUSIONS
All five iodine complexes of amino acids are found to be
two-dimensional (layered) conductors. Most of them reveal band
motion of large polarons in two dimensions consistent with ionic
nature of these charge transfer complexes. Anharmonic
interactions lead to blue shift of vibrations and softening of
phonon modes leads to red shift of vibrations. Two types of
iodine complexes are identified according to the nature of charge
transfer interaction potential.
Ashvin B. Padhiyar / Ph. D. Thesis (Physics) / Sardar Patel University - 2010
262
Table I
Dependence of absorption function on dimensionality. Value of r in = 0
(h - Eg)r / h or = 0 (h - Eg)r
Type of transition Direct Indirect
1 - d 2 - d 3 - d 1 - d 2 - d 3 - d
Allowed
Forbidden
1/2
3/2
0
1
1/2
3/2
2
3
1
2
2
3
Table II
Absorption functions and type of transition in amino acid-iodine
complexes
Name of the
complex
Absorption
function
Type of
transition
Plot
Asparagine - I2 h = A (h - Eg) Forbidden direct
or
Allowed indirect
h vs h
Histidine - I2 = Constant Allowed direct -
Tryptohan - I2 h = A (h - Eg) Forbidden direct
or
Allowed indirect
h vs h
Arginine - I2 = Constant Allowed direct -
Glutamine - I2 = Constant / h Allowed direct vs 1/h
Ashvin B. Padhiyar / Ph. D. Thesis (Physics) / Sardar Patel University - 2010
263
Table III
Gaussian parameters of the Gaussian profiles in amino acid-iodine
complexes.
Name of the Complex Gaussian Parameters
Central wave-
number
(cm- 1)
Absorption
maximum
(%)
FWHM
(cm- 1)
Asparagine - I2
(1)
1900
16.0
1400
Histidine - I2
(1)
(2)
1380
900
22.5
12.5
450
500
Tryptohan - I2
(1)
1350
27.5
1000
Arginine - I2
(1)
1670
15.0
320
Glutamine - I2
(1)
(2)
1650
780
23.0
12.5
200
400
Ashvin B. Padhiyar / Ph. D. Thesis (Physics) / Sardar Patel University - 2010
264
REFERENCES [1] F Gutman and L E Lyons, Organic semiconductors,
John Wiley and Sons, New York, 1967.
[2] Roy Foster, Organic charge transfer complexes, Academic
Press, New York, 1968
[3] S Kanda and K A Pohl in organic semi conducting
polymers, Ed. By J E Katon Marcel Dekker Inc. New York,
1968,p 67
[4] A F Garito and A J Heeger in One-dimensional conducting,
Ed. By H G Schuster,
[5] J J Andre, A-Bieber and F Gautier, Ann de Phy, I, 145,
1967
[6] M A Slifkin, Charge Transfer Interactions in Biomolecules,
Academic Press, London, 1971
[7] D D Eley in organic semiconducting polymers, Ed. By J E
Katon, Marcel Dekker Inc. New York 1968 p.
[8] A Szent – Gyorayi, bioenergetics, Academic Press, New
York, 1957
[9] M A Slifkin, Nature, 193, 464, 1962
[10] J B Birks and M A Slifkin, Nature, 197, 42, 1963
[11] M A Slifkin, Spectrochim, Acta, 20, 1543, 1964 p
[12] M A Slifkin, Nature, 197, 275, 1963
[13] G Weber, Biochem. J, 47,114, 1950
[14] I Isenberg and A Szent – Gyorgyi, Proc Nat. Acad – Sci
(USA), 44,857, 1958
[15] R Beuker and A Szent – Gyorgyi, Rec – Trav. Chim, 81,
541, 1962
[16] E M C Davis, D D Elay and R S Snart, Nature,186, 724,
1960
Ashvin B. Padhiyar / Ph. D. Thesis (Physics) / Sardar Patel University - 2010
265
[17] D D Elay and R S Snart, Biochem, Biophys, Acta 102, 379,
1965
[18] M A Slifkin, Biochim, Biophys – Acta, 103, 365,1965
[19] Ashvin Padhiyar, A J Patel and A T Oza, J. Phys.
Condenced Matter, 19, 486214, 2007
[20] G K Solanki, Anand Amin, Ashvin Padhiyar, A K Ray and
A T Oza, Ind. J. Biochem. Biophys, 45, 421, 2008
[21] C Kittel, Introduction to solid state physics, 7th Edition,
John Wiley & Sons Singapore, New York, Chichester
Brisbane, Toronto, 2004 (p. 108,297)
[22] Vishal Patel, M.Phil. Dissertation, Sardar Patel Univerity,
2010
[23] Pravinsinh Rathod, M. Phil, Dissertation, Sardar Patel
University, 2009
[24] Mukesh B Patel, S G Patel, Rajiv Vaidya and A T Oza, Ind.
J. Phys. B 77, 199,2003
[25] R G Patel, G K Solanki, S M Prajapati and A T Oza, Ind. J.
Phys. A, 78, 471, 2004
[26] G K Solanki, Mukesh Patel and A T Oza, Pragna – Sardar
Patel University, Research Jour.,16, 150, 2008
[27] Ashvin Padhiyar, A J Patel and A T Oza (To be published)