Design and Engineering of Organic Molecules for Customizable
Terahertz Tags
Shaumik Raya, Jyotirmayee Dash
a,c, Kathirvel Nallappan
a, Vaibhav Kaware
b, Nitin Basutkar
b,
Ashootosh Ambadeb, Kavita Joshi
b, Bala Pesala
a,c
aCSIR- Central Electronics Engineering Research Institute, CSIR Madras Complex, Chennai, India
bCSIR- National Chemical Laboratory, Pune, India
cAcademy of Scientific and Innovative Research, CSIR-SERC, Chennai, India
Email: [email protected]
ABSTRACT
Terahertz (THz) frequency band lies between the microwave and infrared region of the electromagnetic spectrum.
Molecules having strong resonances in this frequency range are ideal for realizing "Terahertz tags" which can be easily
incorporated into various materials. THz spectroscopy of molecules, especially at frequencies below 10 THz, provides
valuable information on the low frequency vibrational modes, viz. intermolecular vibrational modes, hydrogen bond
stretching, torsional vibrations in several chemical and biological compounds. So far there have been very few attempts
to engineer molecules which can demonstrate customizable resonances in the THz frequency region. In this paper,
Diamidopyridine (DAP) based molecules are used as a model system to demonstrate engineering of THz resonances (<
10 THz) by fine-tuning the molecular mass and bond strengths. Density Functional Theory (DFT) simulations have been
carried out to explain the origin of THz resonances and factors contributing to the shift in resonances due to the addition
of various functional groups. The design approach presented here can be easily extended to engineer various organic
molecules suitable for THz tags application.
Keywords: Terahertz Spectroscopy, Density Functional Theory (DFT), Diamidopyridine (DAP)
1. INTRODUCTION
Terahertz (THz) radiation is a part of electromagnetic spectrum ranging from 0.1 to 10 THz (with wavelengths from 3
mm to 30 µm). Until recently, this particular frequency region hasn’t been widely explored for commercial applications
due to the unavailability of suitable low cost and high power sources [1]. As a result, THz portion of the electromagnetic
spectrum was referred to as THz gap. Recent developments in continuous wave and time-domain THz systems in
providing wide frequency range THz sources has made THz technology a potential tool for various applications in
medicine, microelectronics, agriculture and security [2].
In order to design THz tags, it is important to understand the vibrational modes contributing to resonances in the THz
frequency range. Studies on THz vibrational modes of various organic molecules have been done to understand the
reason behind these resonances, which are mainly due to intermolecular and intramolecular vibrations, hydrogen bond
stretching and torsional vibrations [3,4]. Of particular interest are the molecules containing hydrogen bonds. Since
hydrogen bond is a weak bond, resonances due to the hydrogen bond stretches occur at lower THz frequencies (< 2
THz), which is of significant interest in the present study towards designing molecules with resonances in lower THz
frequency range. Earlier studies on ATGC, main components of DNA, show that the low frequency vibrational modes
(<4 THz) are dominated by intermolecular hydrogen bond bending [5]. The origin of these resonances is understood by
carrying out density functional theory (DFT) simulations. Ge et al. [6] reported the spectroscopy results of 4-
Hydroxycinnamic acid derivatives in a frequency region between 0.3-2 THz and assigned the individual THz spectra as
scissoring/twisting or stretching of the dimer linked by hydrogen bonds. Biotin and lactose were studied because of the
presence of narrow resonances below 1 THz. Allis et al. have explained the reason behind the lowest THz absorption
signatures in Biotin and Lactose Monohydrate [7]. The narrow THz line shapes of these molecules are due to the
decoupling of single vibrational modes from nearby modes and due to intermolecular interaction in molecular crystals.
DFT simulations of Lactose show that the resonances below 1 THz are mainly due to the rotational motions (0.525 THz)
and intramolecular twisting motions (0.86 THz). Recently, THz spectroscopy has been used to study the hydration
dynamics in various biomolecules [8, 9]. Low frequency vibrations in biomolecules occur in the picosecond time scale
which resonates at THz frequencies. Low frequency modes, especially those found in proteins are linked to large
Terahertz, RF, Millimeter, and Submillimeter-Wave Technology and Applications VII,edited by Laurence P. Sadwick, Créidhe M. O'Sullivan, Proc. of SPIE Vol. 8985, 89850P
2014 SPIE · CCC code: 0277-786X/14/$18 · doi: 10.1117/12.2041194
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vibrations of the molecule. Hydration studies are important to understand the role of water in various bio-chemical and
signaling processes occurring at the cellular level. Based on these studies, it can be inferred that THz resonances are
mainly due to the intermolecular vibrations (in-plane/out-of-plane bending modes).
So far, there have been few studies towards designing and engineering of molecules in the THz region. Molecules with
strong resonances at lower THz frequencies, especially at frequencies < 1 THz, are ideal for realizing THz tags since
very few molecules have resonances in this region. Moreover, these molecular THz tags can be easily incorporated into
various materials/substrates, enabling effective detection of counterfeits in security and pharmaceutical industries [10].
Based on spring-mass methodology, resonances can be fine-tuned either by changing the molecular mass or by changing
the force constant of the intramolecular/intermolecular bonds. Using this principle, we present significant results towards
the design and engineering of various Diamidopyridine (DAP) based molecules which show customizable resonances in
the THz region (< 10 THz). DFT simulations have been carried out to understand the origin of these THz resonances and
factors contributing to the shift in resonances due to the addition of various functional groups [5-7]. The design approach
presented here can be readily extended to design various molecular THz tags.
2. DESIGN OF DIAMIDOPYRIDINE (DAP) BASED MOLECULES
THz resonances can be customized and fine-tuned by including various functional groups, which result in different
molecular mass and/or intramolecular/intermolecular bond strengths. The customization of THz resonances can be linked
to spring-mass analogy. Molecular bonds vibrate in a manner that is similar to a spring-mass system undergoing simple
harmonic motion. Each molecular vibration will have different resonance frequency, which mainly depends on the bond
strength (the spring constant in a spring-mass system) and the reduced mass of the molecule. Using a simple harmonic
oscillator model of a diatomic molecule (A-B), the vibrational frequencies can be calculated as:
1
2
kf
(1)
Where 'k' is the force constant in the atomic scale and the spring constant for macroscopic model respectively, and μ is
the reduced mass given by
.A B
A B
m m
m m
(2)
Where mA and mB are the mass of the atoms in the molecule A-B. The strength of the chemical bond in the molecule A-
B is mainly characterized by the force constant [11]. Therefore, weaker the chemical bond (electronic effect) and larger
the reduced mass μ (mass effect), the lower is the resonance frequency [11]. It implies that, resonance frequencies of in-
plane stretching vibrations in general are higher than those of bending vibrations because the rhythmical movement
along the bond axis is associated with larger force constant compared to the change in the bond angle. Using a similar
analogy, out-of-plane bending vibrations or torsions have lower frequencies than in-plane bending vibrations. By adding
functional groups, the bond strength and the reduced mass can be changed, hence the resonance frequencies in the THz
range (< 5 THz) can be effectively tuned.
Mono-PhDAP N-(6-amidopyridin-2-
yl) benzamide
Pr-PhDAP N-(6-propion
amidopyridin-2-yl)
benzamide
PhDAP (N,N’-(pyridine-2, 6-
diyl) dibenzamide)
4-NO2-PhPhDAP N-(6-benzamido pyridin-2-
yl)-4-nitrobenzamide
Chart 1: Structure of PhDAP and its derivatives
Based on this methodology, THz molecules have been designed having higher molecular mass (mass effect) and tunable
intramolecular/intermolecular bond strengths (electronic effect). In the present study, higher molecular mass has been
realized by considering molecules with multiple aromatic rings and lower force constant has been achieved by adding
various functional groups. Electronegative atoms such as Nitrogen are incorporated in the aromatic structures (called
heterocyclic structures) instead of only benzene rings in order to vary the bond strength easily. Functional groups
containing Nitrogen are integrated on minimum of two positions of the heterocyclic ring to realize multiple
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intramolecular/intermolecular hydrogen bonds. Molecules either with two aromatic rings (Mono-PhDAP) and its
derivative (Pr-PhDAP) or with three aromatic rings (PhDAP) and its derivative (4-NO2Ph-PhDAP) have been
synthesized using this design. Chart 1 shows the molecular structure of these molecules.
3. THZ SPECTROSCOPY OF DIAMIDOPYRIDINE BASED DERIVATIVES
The primary focus of the study is to investigate the effect of changing molecular mass and the force constant on the THz
resonances. Mono-PhDAP has been chosen as the base molecule and hydrogen atom of –NH2 group has been replaced
with CO-CH2-CH3 in Pr-PhDAP to observe the change in resonance due to its addition. Similarly, one more aromatic
ring has been added to Mono-PhDAP to change the molecular mass significantly. Further, hydrogen atom at 4th
position
in PhDAP is replaced with –NO2 to observe the change in resonance due to change in the bond strength and reduced
mass. These four molecules have been designed and synthesized using the following general procedure.
3.1 Synthesis of PhDAP
In a round bottom flask, 2,6‐diamidopyridine (1g, 9.163 mmol) was dissolved in 40mL of dry dichloromethane and
triethylamine (2.8mL, 27.72mmol) was added. Then, benzoyl chloride (2.5 mL, 17.98 mmol) was added drop by drop
and this mixture was stirred under inert atmosphere at room temperature for 15h. Reaction mixture was poured in water.
Crude product was extracted in dichloromethane, organic layer was washed with water and dried over anhydrous sodium
sulphate. The solvent was evaporated on rotary evaporator and crude product was purified by column chromatography
on silica gel by eluting with ethyl acetate: hexane (40:60) mixture. The product was further purified by recrystallization
using methanol. Similarly, other molecules have also been synthesized with high purity.
3.2 Sample Preparation
Powdered samples suitable for THz spectroscopy were prepared by mixing with high density polyethylene (HDPE) in
the ratio of roughly 30:70 by concentration. Smooth pellets with a thickness of 1 mm were prepared after applying a
pressure of 15 tonnes in a Potassium Bromide (KBR) press unit for 2 minutes. The samples have been scanned in a
Nicolet 6700, Thermo-Scientific instrument capable of taking THz measurements over a wide frequency range (2 THz to
21 THz). The spectrum obtained is averaged for 36 times with a spectral resolution of 4 cm-1
.
3.3 Terahertz Spectroscopy results
Figure 1(a) shows comparison of experimental spectra of Mono-PhDAP and Pr-PhDAP and fig. 1(b) shows the
comparison of experimental spectra of PhDAP and 4-NO2Ph-PhDAP. Experiments have been carried out with two
pellets of each chemical in order to verify the repeatability of the results. The experimental results show significant
differences in the THz resonances both in the shape of the spectrum and in the position of the peaks due to the change in
chemical structure of the molecules. This change in resonances can be attributed to the change in the molecular masses
and strength of intermolecular/intramolecular bonds.
Fig.1(a): Comparison of experimental THz spectra of Mono-
PhDAP and Pr-PhDAP
Fig. 1(b): Comparison of experimental THz spectra of PhDAP
and 4-NO2Ph-PhDAP
2 3 4 5 6 7 8 9 100.2
0.4
0.6
0.8
1
Frequency(THz)
Ab
so
rba
nc
e (
a.u
)
Pr-PhDAP
Mono-PhDAP
**
*
*
2 3 4 5 6 7 8 9 100.2
0.4
0.6
0.8
1
Frequency(THz)
Ab
so
rba
nc
e (
a.u
)
PhDAP
4NO2-Ph-PhDAP
*
*
*
***
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From fig. 1(a) it is seen that, resonances are changed by replacing hydrogen in –NH2 with CO-CH2-CH3, in Mono-
PhDAP structure. Similarly, fig. 1(b) shows the shift in resonances due to addition of –NO2 to PhDAP structure. The
resonances having the same mode of vibration, as discussed in the simulation results below, have been compared and are
marked in the figure. Interestingly, some of the resonances are shifted to lower frequencies while some are shifted to
higher frequencies. Here, we attempt to explain this behaviour by quantifying the relative contribution of two important
factors: mass effect and force constant effect. To understand the contribution of each of these effects, DFT simulations
using Gaussian 09 package [12] have been carried out.
4. DFT SIMULATION RESULTS
Over the years, DFT calculations have become an effective tool to predict molecular structures, charge transfer
interactions as well as intermolecular and intramolecular vibrations. DFT calculations are carried out using hybrid
functional Becke-3-Lee-Yang-Parr (B3LYP) method. The valence double-zeta polarized basis set with six d-type
Cartesian-Gaussian polarization functions (6-31G (d)) was found to give converged results [3]. Here, DFT simulations
have been carried out by considering single molecule and the results are compared with experiments. The results agree
well at higher frequencies (> 5 THz). In future, DFT simulations will be extended to simulate the molecules including
their full crystal structure for accurate prediction of resonances especially at lower THz frequencies.
5. ANALYSIS OF THZ RESONANCES
5.1 Comparison of Mono-PhDAP and Pr-PhDAP
Comparison of experimental and simulated spectra of Mono-PhDAP and Pr-PhDAP are shown in fig. 2(a) and 2(b)
respectively.
Fig. 2(a): Comparison of experiments and DFT simulation
results of Mono-PhDAP
Fig. 2(b): Comparison of experiments and DFT
simulation results of Pr-PhDAP
From the figures, it can be seen that the simulation results match relatively well at higher frequencies (> 5 THz)
compared to lower THz frequencies. This is expected since prediction of resonances at low frequencies resulting from
intermolecular vibrations would need full crystal simulations.
Table1: Comparison of experimental and simulated resonances of Mono-PhDAP and Pr-PhDAP
2 4 6 8 100
0.2
0.4
0.6
0.8
1
Frequency (THz)
Ab
so
rban
ce (
a.u
)
Experiments
Simulations
2 4 6 8 100
0.2
0.4
0.6
0.8
1
Frequency (THz)
Ab
so
rban
ce(a
.u)
Experiments
Simulations
Mono-PhDAP Pr-PhDAP
Experimental
resonances (THz)
Simulated
resonances (THz)
Experimental
resonances (THz)
Simulated
resonances (THz)
2.72 2.71 2.6 2.61
5.09 4.98 3.64 3.59
6.36 6.56 4.80 5.05
8.51 8.26 7.06 6.37
9.95 9.72 8.45 8.67
9.37 9.36
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For the purpose of understanding the origin of THz resonances, we have only considered resonances which are in
reasonable agreement with the DFT simulations. These are 2.72 (2.71 THz), 5.09 (4.98 THz), 6.36 (6.56 THz), 8.51
(8.26 THz) and 9.95 (9.72 THz) in case of Mono-PhDAP. Similarly for Pr-PhDAP, the closely matching frequencies are
2.6 (2.61 THz), 3.64 (3.59 THz), 4.80 (5.05 THz), 7.06 (6.37 THz), 8.45 (8.67 THz) and 9.37 (9.36 THz). Table 1 shows
the comparison of experiments and DFT simulation results of Mono-PhDAP and Pr-PhDAP.
Figure 3 shows how the resonance frequency having same mode of vibration is changed by replacing hydrogen in –NH2
with -CO-CH2-CH3 in Mono-PhDAP structure. It is observed that Pr-PhDAP has lower resonance frequency compared to
Mono-PhDAP around 2 THz. Comparisons between the molecules have been done at lower frequencies since the
eventual goal of this study is to design organic molecules with resonances below 1 THz (even though experimental
results below 2 THz are unavailable at present as it is beyond the capability of our instrument). To understand the reason
behind shift in frequencies, the exact mode of vibration has been examined, which is shown in fig. 3(a) and 3(b).
Fig. 3(a): Mode of vibration of monoPhDAP at
2.09 THz (69.66 cm-1)
Fig. 3(b): Mode of vibration of PrPhDAP at
1.81 THz (60.49 cm-1)
This is primarily an out-of-plane bending vibration of the two Pyridine rings about the N-C bond. In addition, there is
also twisting of oxygen and nitrogen atom across carbon atom. Pr-PhDAP has a lower resonance mainly due to the
decrease in force constant from 0.017 to 0.012 N/m as given in table 2. Interestingly, inspite of increase in the molecular
mass, reduced mass of Pr-PhDAP is less than that of Mono-PhDAP in this mode of vibration. Further studies are needed
to understand the reasons behind the reduction in the reduced mass. We have also compared other resonances (below 10
THz) to understand the origin of the differences in resonance frequencies in table 2.
Table 2: Comparison of resonances of monoPhDAP and Pr-PhDAP and the mode of vibration at these frequencies
Mono-PhDAP
PrPhDAP
Force
constant (k)
(N/m)
Reduced
mass (μ)
(amu)
Resonant
frequency
(THz)
Force
constant (k)
(N/m)
Reduced
mass (μ)
(amu)
Resonant
frequency
(THz)
Reason behind the
resonances
0.017 5.93 2.09 0.012 5.55 1.81
Out of plane bending of
the molecule with slight
twisting of N and O
across C
0.078 4.83 4.98 0.082 4.93 5.05
Out of plane bending of
both the rings due to C=O
oscillations
0.342 5.51 9.72 0.362 6.32 9.36
In-plane bending of both
the rings due to C=O
oscillations
The second compared frequency which is near 5 THz in case of Pr-PhDAP is due to higher force constant of Pr-PhDAP
compared to Mono-PhDAP. The reduction in resonance of Pr-PhDAP (9.36 THz) compared to Mono-PhDAP (9.72 THz)
is mainly due to the increase in the reduced mass. In summary, from the simulation results, shift in the resonances to
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higher or lower frequencies upon adding a functional group can be clearly explained as a spring constant effect or
reduced mass effect. Detailed experimental studies are planned in order to better understand the mass/spring constant
effects by replacing/adding a single atom in the same molecular structure.
5.2 Comparison of PhDAP and 4-NO2Ph-PhDAP
In order to increase the reduced mass, structure with three aromatic rings (PhDAP) and its derivative 4-NO2Ph-PhDAP
have been synthesized and characterized using THz spectroscopy. Comparison between PhDAP and its derivative 4-
NO2Ph-PhDAP shows how the resonances are changing by adding the electron-withdrawing functional group (–NO2) to
PhDAP molecule. Figures 4(a) and 4(b) show the experimental and simulated spectra of PhDAP and 4-NO2Ph-PhDAP
respectively.
Fig. 4(a): Comparison of THz experiments and DFT
simulation spectra of PhDAP.
Fig. 4(b): Comparison of THz experiments and DFT
simulation spectra of 4-NO2Ph-PhDAP
Similar to the analysis in the case of Mono-PhDAP compounds, we have considered the frequencies which are matching
closely with simulation results. The matched frequencies in PhDAP are 2.6 (2.86 THz), 5.15 (5.24 THz), 5.61 (5.57
THz), 7.35 (7.24 THz), 8.16 (8.36 THz), 8.79 (9.05 THz). Similarly, for 4-NO2Ph-PhDAP, the matched frequencies are
2.95 (3 THz), 4.51 (4.72 THz), 4.8 (5.08 THz), 5.55 (5.22 THz), 6.94 (6.78 THz), 8.39 (8.57 THz) and 9.08 (8.97 THz)
which is given in table 3.
Table3: Comparison of experimental and simulated resonances of PhDAP and 4-NO2Ph-PhDAP
By comparing the lowest mode of vibration of mono-PhDAP and PhDAP, we can see that PhDAP (1.89 THz) has lower
resonance as compared to Mono-PhDAP (2.09 THz). This is clearly due to the increase in reduced mass since the force
constant of both molecules are same (as seen in table 2 and 4). From the simulations, we also observe that 4-NO2Ph-
PhDAP has lower resonance frequency compared to PhDAP at around 1.8 THz. To understand the origin of this
resonance, the exact mode of vibration has been investigated, which is shown in fig. 5(a) and 5(b).
2 3 4 5 6 7 8 9 100
0.2
0.4
0.6
0.8
1
Frequency (THz)
Ab
so
rba
nc
e(a
.u)
Simulations
Experiments
2 3 4 5 6 7 8 9 100
0.2
0.4
0.6
0.8
1
Frequency (THz)A
bs
orb
an
ce
(a
.u)
Experiments
Simulations
PhDAP 4-NO2Ph-PhDAP
Experimental
resonances (THz)
Simulated
resonances (THz)
Experimental
resonances (THz)
Simulated
resonances (THz)
2.6 2.86 2.95 3
5.15 5.24 4.51 4.72
5.61 5.57 4.8 5.08
7.35 7.24 5.55 5.22
8.16 8.36 6.94 6.78
8.79 9.05 8.39 8.57
9.08 8.97
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Fig. 5(a): Mode of vibration of PhDAP at
1.89 THz (63.11cm-1)
Fig. 5(b): Mode of vibration of 4-NO2Ph-PhDAP at
1.73 THz (57.72 cm-1)
The mode of vibration shown in fig. 5(a) and 5(b) is primarily an out of plane bending of the molecule due to twisting of
Oxygen and Nitrogen across the Carbon atom. The resonance frequency of 4-NO2Ph-PhDAP is less as compared to
PhDAP due to lower force constant which is given in table 4. We have also compared other resonances (below 10 THz)
to understand the origin of the differences in resonance frequencies between these molecules.
Table 4: Comparison of resonances of PhDAP and 4-NO2-Ph-PhDAP and the mode of vibration at these frequencies
PhDAP
4-NO2-Ph-PhDAP
Force
constant (k)
(N/m)
Reduced
mass (μ)
(amu)
Resonant
frequency
(THz)
Force
constant (k)
(N/m)
Reduced
mass (μ)
(amu)
Resonant
frequency
(THz)
Reason behind the resonances
0.017 7.38 1.89 0.014 7.07 1.73
Out of plane bending of the
molecule due to twisting of O
and N across C
0.115 5.68 5.57 0.098 5.49 5.22
Out of plane bending of the
middle and one side ring and in-
plane bending of the other
aromatic ring
0.196 5.71 7.24 0.191 6.33 6.78 In-plane bending of each of the
aromatic rings
0.367 6.84 9.05 0.371 7.04 8.97
In-plane bending of the
peripheral rings and out of plane
bending of middle ring
From table 4, the resonance frequency of 4-NO2Ph-PhDAP (around 5 THz) is less than that of PhDAP, which is mainly
due to the reduction in the force constant whereas lowering of the third resonance frequency (7 THz) is mainly due to the
increase in reduced mass. PhDAP has higher resonance around 9 THz mainly due to lower reduced mass of PhDAP than
4-NO2Ph-PhDAP. The resonances (with same vibrational mode) are shifted to lower frequencies due to the addition of
electronegative group (-NO2) to the PhDAP structure and is validated by the change in spring constant to reduced mass
ratio.
Binary molecular complexes with intermolecular hydrogen bonds have also been synthesized based on PhDAP
derivatives. The primary aim of this study is to realize resonances much lower than the resonances achieved with single
molecule. Preliminary results show that the Terahertz resonances can be further fine-tuned using this approach as the two
molecules in a binary complex are connected with intermolecular hydrogen bonds. Comparison of the resonances of the
complexes and individual molecules shows similar trends in the change of Terahertz resonances.
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6. CONCLUSION
THz resonance frequencies of PhDAP based derivatives have been successfully customized by tuning the bond strengths
and by varying the molecular mass. We have been able to show both experimentally as well as with simulations, how the
THz resonances can be varied by adding more electronegative functional groups which is evident in the case of PhDAP
and 4-NO2Ph-PhDAP. Further, we have qualitatively explained the relative contribution of two important factors: mass
effect and force constant effect. To understand contribution of each of these effects, Density Functional Theory (DFT)
simulations have been carried out. This approach can be easily extended towards designing THz molecules, which can
show sharp prominent resonances below 1 THz suitable for realizing THz tags.
ACKNOWLEDGEMENTS
The authors like to thank Director General, CSIR and Director, CSIR-CEERI for their invaluable support throughout the
research work. Part of the research work has been carried out with equipment of CSIR innovation Complex for which
authors would like to thank Director, CSIR-SERC. Authors would also like to thank SIC, CEERI Chennai for his kind
support. Authors would like to acknowledge the financial support for this work through CSIR under network project
CSC-0128 (FUTURE).
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