CHAPTER 2
PURINES & PYRIMIDINES
CHAPTER 2
INFRARED SPECTROSCOPY OF CHARGE TRANSFER
COMPLEXES OF PURINES AND PYRIMIDINES
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2.1
PURINES & PYRIMIDINES
Introduction
There is a lot of interest among solid state physicists to study organic
semiconductors [1]. These materials are usually organic charge transfer complexes [2].
Studies on organic compounds are also extended to study biochemical materials [3].
However, studies on CTCs of biomolecules are limited [4]. Recently, we have started
work on solid state spectroscopy of CTCs of biomolecules [5-7]. Charge transfer
induced hydrogen bonding was recently suggested for CTCs of amino acids [8]. Most
of the CTCs of small molecules show that the interband transition is direct [9] while
those of macromolecules show that transition is indirect [10]. When there is discrete
hydrogen bonding such as the one existing in quinhydrone, the transition is found to be
indirect due to local strain in the lattice [11]. Here we report such a local H-bonding
which is induced by charge transfer leading to an indirect transition in the CTCs of
purines and pyrimidines.
2.2
Experimental details
Purines and pyrimidines namely adenine, guanine, thymine, cytosine and uracil
were obtained from chemical company. These white powders were grinded after mixing
with organic acceptors such as TCNE (tetracyano-p-ethylene), TCNQ (7, 7, 8, 8tetracyano-p-quinodimethane),
DDQ
(2,3-dichloro-5,6-dicyano-p-benzoquinone),
chloranil and iodine. The CTCs were further grinded with dry KBr spectrograde powder
to form homogeneous fine powder and palates were prepared by compressing in
manually operated machine. These semitransparent circular discs were used as
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specimens for recording FTIR spectra. The spectrophotometer was constructed by
Perkin Elmer Comply, USA.
The spectrophotometer has resolution of 0.15cm-1, a scan range of 15,600-30 cm1
, a scan time 20 scan sec-1, an OPD velocity of 0.20 cmsec-1 and MIRTCS and FIRTGS
detectors. A beam slitter of opt KBr type was used having a range of 7800-370cm-1.
The spectra were recorded in purge mode.
2.3
Result and discussion
The FTIR spectra in the full infrared range for CTCs of adenine are shown in
figure 2.1a-f. Although adenine transmits infrared light because of its insulating
character, the CTCs of adenine show a range of nature of transitions because of small
band gap semiconducting nature with band gap lying in IR rage. Adenine-TCNQ shows
a nature of transition with band gap around 1800cm-1. The spectrum also shows a
gaussian background profile centered around 700cm-1. The interband transition is found
to be forbidden indirect transition by straight line plot of (Ahν)1/3 vs hν which shows in
figure 2.1g.Gaussian distribution is fitted by plotting lnA vs (k-k0)2 as shown in figure
2.1h. Adenine-TCNE also shows forbidden indirect transition as shown in figure 2.1i. It
is also shows a Gaussian distribution in low-frequency range as shown in figure 2.1j.
Adenine- DDQ reveals a similar transition of nature of transition and a half-Gaussian as
shown in figure 2.1k and figure 2.1 l respectively. Adenine-chloranil also shows
forbidden indirect transition (fig 2.1m) but no Gaussian profile in any range. Adenineiodine shows two regions of interband transition one with band gap of 0.225eV and the
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other one at 0.135eV which shows in figure 2.1n and figure 2.1 o respectively.
respectively It also
shows
ows a Gaussian band (Fig. 2.1p
2.1p). Thus adenine-iodine
iodine complex shows a two band
transport and the charge transfer most probably takes place along iodine chains.
Figure 2.1a The FTIR spectrum of adenine only
Fig 2.1b FTIR spectra of adenine--TCNQ CTC
Fig 2.1c FTIR spectra of adenine-TCNE
TCNE CTC
Fig 2.1d FTIR spectra of adenine-DDQ
adenine
CTC
Fig 2.1e FTIR spectra of adenine-chloranil
chloranil CTC
Fig 2.1f FTIR spectra of adenine-iodine
adenine
CTC
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1.7
2.5
2.3
1.6
2.1
1.9
lnA
(Ahν)1/3
1.5
1.7
1.5
1.4
1.3
1.3
1.1
0.9
1.2
0.7
0.5
1.1
0.22
0.27
hν(eV)
0
0.32
20000
40000
60000
)2
(k-k0
Figure 2.1g Nature of transition in Adenine-TCNQ
Figure 2.1h Gaussian distribution in Adenine-TCNQ
3
2.5
2.8
2.6
2
2.4
2.2
lnA
(Ahν)1/3
1.5
2
1.8
1
1.6
1.4
0.5
1.2
1
0
0
0.22
0.27
0.32
10000 20000 30000 40000
0.37
(k-k0)2
hν(eV)
Figure 2.1i Adenine-TCNE Nature of transition
Figure 2.1j Adenine-TCNE (Gaussian)
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2.1
1.7
lnA
(Ahν)1/3
1.9
1.5
1.3
1.1
0.9
0.7
0.24
0.29
hν(eV)
150000 200000 250000 300000 350000
0.34
(k-k0)2
Figure 2.1k Adenine-DDQ (NT)
Figure 2.1 l Adenine-DDQ (Gaussians)
3
(Ahν)1/3
(Ahν)1/3
2.5
2
1.5
1
0.24
2.7
2.6
2.5
2.4
2.3
2.2
2.1
2
1.9
0.29
0.34
2.1
1.9
1.7
1.5
1.3
1.1
0.9
0.7
0.22
hν(eV)
Figure 2.lm Adenine-chloranil nature of transition
0.27 hν(eV) 0.32
0.37
Figure 2.1n Nature of transition in Adenine-iodine at
o.22eV band gap
2.5
1.6
2
1.4
lnA
(Ahν)1/3
1.5
1.5
1.3
1.2
1
1.1
1
0.5
0.13
0.15
0.17
hν(eV)
0.19
0.21
Figure 2.1 o Nature of transition in Adenine-iodine
at o.13eV band gap
0
20000
40000
(k-k0)2
60000
Figure 2.1p Adenine-iodine Gaussian
The FTIR spectra of guanine and its CTCs with standard organic acceptors are
shown in figure 2.2a-f. Guanine alone transmits light in the mid-IR range indicating its
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insulating nature. All of the CTCs of guanine with TCNQ, TCNE, DDQ, chloranil and
iodine reveal forbidden indirect transitions from plots of (Ahν)1/3 vs hν which are
straight lines as show in figure 2.2g-k. Gaussian distributions are found in TCNQ, DDQ
and iodine complexes which are fitted as shown in figure 2.2 l-n as lnA vs (k-k0)2 .
Guanine-chloranil complex shows a half power beta density i.e. α = α0k*1/2(1-k*)1/2 ,
indicating a hopping transport of charge carriers as shown in figure 2.2o .
Figure 2.2a FTIR spectra of guanine only
Figure 2.2c The FTIR spectra of guanine-TCNE CTC
Figure 2.2b The FTIR spectra of guanine-TCNQ CTC
Figure 2.2d The FTIR spectra of guanine-chloranil CTC
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Figure 2.2e The FTIR spectra of guanine-DDQ CTC
Figure 2.2f The FTIR spectra of guanine-iodine CTC
1.8
1.7
(Ahυ)1/3
(Ahυ)1/3
1.6
1.5
1.4
1.3
1.2
1.1
1
0.22
0.27
hν (eV)
0.24
0.32
Figure 2.2g Nature of transition in guanine-TCNQ CTC
2
1.6
1.8
1.5
1.6
1.4
1.4
1.2
1
1.1
0.8
1
0.3
0.32
hν (eV)
0.34
Figure 2.2i Nature of transition in guanine-DDQ CTC
0.34
1.3
1.2
0.28
0.29
hν(eV)
Figure 2.2h Nature of transition in guanine-TCNE CTC
(Ahυ)1/3
(Ahυ)1/3
2.3
2.1
1.9
1.7
1.5
1.3
1.1
0.9
0.7
0.5
0.24
0.26
0.28
hν (eV)
0.3
0.32
Figure 2.2j Nature of transition in guanine-chloranil CTC
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3
2.1
2.5
2
2
1.9
lnA
(Ahν)1/3
CHAPTER 2
1.5
1.8
1
1.7
0.5
1.6
0
1.5
0.24
0.26
0.28
0.3
0.32
0
0.34
10000
(k-k0)2
hν(eV)
Figure 2.2 l Gaussian distribution in guanine-TCNQ CTC
0.7
3.5
0.6
3
0.5
2.5
0.4
2
lnA
lnA
Figure 2.2k Nature of transition in guanine-iodine CTC
0.3
1.5
0.2
1
0.1
0.5
0
0
0
50000 100000 150000 200000
20000
0
(k-k0)2
5000
10000
15000
20000
(k-k0)2
Figure 2.2m Gaussian distribution in guanine-DDQ CTC
Figure 2.2n Gaussian distribution in guanine-iodine CTC
12
10
The Infrared spectra of thymine and
A
8
its CTCs are shown in figure 2.3a-f. TCNQ,
6
4
TCNE, DDQ, chloranil and iodine complexes
2
again show forbidden indirect transitions
0
0
0.2
0.4
k*1/2(1-k*)1/2
Figure 2.2 o Half-power beta density in guaninechloranil CTC
0.6
with Ahν=B(hν-Eg±Ep)3 as the best fitted as
shown in figure 2.3g-k. Thymine-DDQ and
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thymine-chloranil also shows Gaussian distributions which is fitted as shown in figure
2.3l-m.
Figure 2.3a FTIR spectra of thymine only
Figure 2.3c FTIR spectra of thymine-TCNE CTC
Figure 2.3e FTIR spectra of thymine-DDQ CTC
Figure 2.3b FTIR spectra of thymine-TCNQ CTC
Figure 2.3d FTIR spectra of thymine-chloranil CTC
Figure 2.3f FTIR spectra of thymine-iodine CTC
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1.8
1.7
1.6
1.5
1.4
1.3
1.2
1.1
1
0.9
0.8
1.5
1.4
1.3
(Ahν)1/3
(Ahν)1/3
CHAPTER 2
1.2
1.1
1
0.9
0.8
0.22
0.27
0.32
0.37
0.22
0.27
hν(eV)
hν(eV)
Figure 2.3h Nature of transition in thymine-TCNE CTC
2
2.2
1.8
2
1.6
1.8
(Ahυ)1/3
(Ahν)1/3
Figure 2.3g Nature of transition in thymine-TCNQ CTC
1.4
1.2
1.6
1.4
1
1.2
0.8
1
0.25
0.27
0.29
0.31
0.33
0.24
0.26
0.28
0.3
0.32
hν (eV)
hν (eV)
Figure 2.3i Nature of transition in thymine-DDQ CTC
(Ahυ)1/3
0.32
Figure 2.3j NT in thymine-chloranil CTC
1.6
1.5
1.4
1.3
1.2
1.1
1
0.9
0.8
0.7
0.6
0.27
0.29
0.31
0.33
0.35
hν (eV)
Figure 2.3k Nature of transition in thymine-iodine CTC
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PURINES & PYRIMIDINES
3.3
3
3.1
2.8
2.9
2.6
2.7
2.4
2.5
2.2
lnA
lnA
CHAPTER 2
2.3
2
2.1
1.8
1.9
1.6
1.7
1.4
1.5
1.2
0
50000
100000
150000
0
(k-k0)2
Figure 2.3l Gaussian distribution in thymine-DDQ CTC
100000
200000
300000
(k-k0)2
Figure 2.3m Gaussian distribution in thymine-chloranil CTC
The FTIR spectra of cytosine and its CTCs are shown are shown in figure 2.4a-f.
(Ahν)1/3 vs hν plots are again found to be straight lines indicating that the transitions are
forbidden indirect type which are shown in figure 2.4g-k. Cytosine-chloranil shows two
gaussian bands and are fitted as shown in figure 2.4l- m.
Figure 2.4a FITR spectra of cytosine only
Figure 2.4b FTIR spectra of cytosine-TCNQ CTC
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Figure 2.4c FTIR spectra of cytosine-TCNE CTC
Figure 2.4d FTIR spectra of cytosine-chloranil CTC
Figure 2.4e FTIR spectra of cytosine-DDQ CTC
Figure 2.4f FTIR spectra of cytosine-iodine CTC
2.5
(Ahν)1/3
(Ahν)1/3
2
1.5
1
0.5
0
0.22
0.27
0.32
0.37
2.5
2.3
2.1
1.9
1.7
1.5
1.3
1.1
0.9
0.7
0.22
hν (eV)
Figure 2.4g Nature of transition in cytosine-TCNQ CTC
CTC
0.27
0.32
0.37
hν (eV)
Figure 2.4h Nature of transition in cytosine-TCNE
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(Ahν)1/3
(Ahν)1/3
2.5
2.3
2.1
1.9
1.7
1.5
1.3
1.1
0.9
0.7
0.5
0.22
0.27
0.32
2.5
2.3
2.1
1.9
1.7
1.5
1.3
1.1
0.9
0.7
0.37
0.24
hν (eV)
Figure 2.4i Nature of transition in cytosine-chloranil CTC
0.29
hν (eV)
0.34
0.39
Figure 2.4j Nature of transition in cytosine-DDQ CTC
1.6
1.4
1.2
1
0.8
0.6
0.4
0.2
0
3
2.8
lnA
(Ahν)1/3
3.2
2.6
2.4
2.2
2
0
0.22
0.23
0.24
hν (eV)
0.25
100000
150000
(k-k0)2
Figure 2.4k Nature of transition in cytosine-iodine CTC
lnA
50000
0.26
Figure 2.4l Gaussian distribution in cytosine-chloranil CTC
3.5
3
2.5
2
1.5
1
0.5
0
0
10000
(k-k0)2
20000
30000
Figure 2.4m Gaussian distribution in cytosine-chloranil CTC
Finally the IR spectra of uracil and its CTCs are shown in figure fig 2.5a-f.
Natures of transition of CTCs of uracil are fitted as shown in figure 2.5g-k. UracilTCNQ, uracil-TCNE and uracil-chloranil reveal allowed indirect transitions by fitting
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ahν=B(hν-Eg±Ep)2. Uracil-DDQ and uracil-iodine reveal forbidden indirect type
transition. Only uracil-chloranil shows a gaussian band which fitted as in figure 2.5 l.
Figure 2.5a FTIR spectrum of uracil only
Figure 2.5b FTIR spectrum of uracil-TCNQ CTC
Figure 2.5c FTIR spectrum of uracil-TCNE CTC
Figure 2.5d FTIR spectrum of uracil-chloranil CTC
Figure 2.5e FTIR spectrum of uracil-DDQ CTC
Figure 2.5f FTIR spectrum of uracil-iodine CTC
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PURINES & PYRIMIDINES
2.2
2.4
2.15
2.2
(Ahν)1/2
(Ahν)1/2
CHAPTER 2
2.1
2
2.05
1.8
2
1.6
1.4
1.95
1.2
1.9
1
1.85
0.24
0.2
0.25
0.3
0.35
0.34
hν(eV)
hν(eV)
Figure 2.5g Nature of transition in uracil-TCNQ CTC
0.29
Figure 2.5h Nature of transition in uracil-TCNE CTC
1.8
3
1.7
2.5
(Ahν)1/2
(Ahν)1/3
1.6
1.5
1.4
2
1.5
1.3
1
1.2
0.5
1.1
0
1
0.24
0.29
0.34
0.24
0.34
hν(eV)
hν(eV)
Figure 2.5i Nature of transition in uracil-DDQ CTC
0.29
Figure 2.5j Nature of transition in uracil-chloranil CTC
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PURINES & PYRIMIDINES
2.5
3
2
2.5
lnA
(Ahν)1/3
CHAPTER 2
1.5
1
2
1.5
1
0.5
0.5
0
0
0.25
0.3
hν(eV)
0.35
Figure 2.5k Nature of transition in uracil-iodine CTC
0
100000
200000
(k-k0)2
300000
Figure 2.5l Gaussian distribution in uracil-chloranil CTC
Most of the CTCs of small donor molecules with standard organic acceptors
show that the interband transition is either allowed or forbidden but always direct [10].
However, macromolecules when form CTCs with standard acceptors show indirect
transitions [5]. When there is discrete hydrogen bonding such as the one existing in
quinhydrone, the transition is found to be indirect due to local strain in the lattice [11].
Charge transfer induced hydrogen bonding and global network of infinite number of
hydrogen bond spanning the whole crystal leading to direct transitions are proposed
recently for four amino acids, namely asparagines, arginin, histidine, and glutamin [8].
Here, we have studied purines and pyrimidines to check whether their CTCs are onedimensional or two-dimensional semiconductors. It is found that only discrete hydrogen
bonding seems to exist which is inducted by charge transfer because the transition is
indirect. Thus purines and pyrimidines form hydrogen bonded dimmers with N-H--N or
N-H--O type hydrogen bonding. Also there is possibility of N-H--π hydrogen bonding
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because of π-characters of the organic acceptors. All transitions are summarized in
table-2.1. Transitions are forbidden because of large intermolecular distance.
2.4
Conclusion
The charge transfer complexes of purines and pyrimidines namely adenine,
guanine, thymine, cytosine and uracil with standard organic acceptors such as TCNQ,
TCNE, DDQ, chloranil and iodine all show indirect transitions in spite of being small
molecules. Thus there is local hydrogen bonding forming dimmers of the donors. The
CT interaction is not strong enough to induce global hydrogen bonded network which
would show direct transitions. CTCs are not two-dimensional but remain threedimensional. Band gap is a non-universal Hubbard gap rather than a Peierls gap.
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Table 2.1: Nature of transition in CTCs of purines and pyrimidines
Name of the complex
Adenine-TCNQ
Adenine-TCNE
Adenine-DDQ
Adenine-chloranil
Adenine-Iodine
Guanine-TCNQ
Guanine-TCNE
Guanine-DDQ
Guanine-chloranil
Guanine-Iodine
Thymine-TCNQ
Thymine -TCNE
Thymine -DDQ
Thymine -chloranil
Thymine -Iodine
Cytosine-TCNQ
Cytosine -TCNE
Cytosine -DDQ
Cytosine -chloranil
Cytosine -Iodine
Uracil-TCNQ
Uracil-TCNE
Uracil-DDQ
Uracil-chloranil
Uracil-Iodine
Absorption function
Ahν=B(hν-Eg±Ep)3
Do
Do
Do
Do
Do
Do
Do
Do
Do
Do
Do
Do
Do
Do
Do
Do
Do
Do
Do
Ahν=B(hν-Eg±Ef)2
Ahν=B(hν-Eg±Ef)2
Ahν=B(hν-Eg±Ep)3
Ahν=B(hν-Eg±Ep)2
Ahν=B(hν-Eg±Ep)3
Nature of transition
Forbidden indirect
Forbidden indirect
Forbidden indirect
Forbidden indirect
Allowed indirect
Allowed indirect
Forbidden indirect
Allowed indirect
Forbidden indirect
Band
gap
Eg(eV)
0.230
0.220
0.240
0.250
0.225
0.240
0.250
0.285
0.245
0.250
0.240
0.240
0.252
0.257
0.278
0.240
0.240
0.252
0.244
0.223
0.235
0.252
0.242
0.255
0.270
References
1. F. Gutman and L.E.Lyos, Organin Semiconductors, John Wiley and Sons, Inc.,
1967.
2. Roy Foster, Organic Charge Transfer Complexes, Academic Press, New York,
1969.
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CHAPTER 2
PURINES & PYRIMIDINES
3. M.A.Slifkin, Charge Transfer Interactions of Biomolecules, Academic Press,
London, 1971.
4. D.D. Eley in Organic Semiconducting Polymers, Ed. By J.E.Katon, Marcel
Dekker Inc., New York, 1968.
5. Ashvin B. Padhiyar, M.Phil. Dissertation, Sardar Patel University, Vallabh
Vidyanagar, 2003.
6. Pravinsinh I. Rathod, M.Phil. Dissertation, Sardar Patel University, Vallabh
Vidyanagar, 2009.
7. Vishal B. Patel, M.Phil. Dissertation, Sardar Patel University, Vallabh
Vidyanagar, 2010.
8. Ashvin B. Padhiyar, A. J. Patel and A. T. Oza, J. Phys. Condensed Matter, 19,
486214, 2007.
9. R.G.Patel, G.K.Solanki, S.M.Prajapati and A.T.Oza, Indian J.Phys., 78A, 471,
2004.
10. Ashvin B. Padhiyar, Ph.D. Thesis, Sardar Patel University, Vallabh Vidyanagar,
2011.
11. Parimal Trivedi, Ashok Patel, R.G.Patel, V.A. Patel and A.T.Oza, Ind. J. Pure and
App. Phys., 43, 335,2005.
Pravinsinh I. Rathod/Ph.D. Thesis (Physics)/S.P.U., V.V.Nagar-2013
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