Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy 219 (2019) 23–32

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Spectrochimica Acta Part A: Molecular and Biomolecular

Spectroscopy
journal homepage: www.elsevier.com/locate/saa

The deconvolution analysis of ATR-FTIR spectra of diacetylene during

UV exposure
Roberto D. Ortuso, Niccolò Ricardi, Thomas Bürgi, Tomasz A. Wesolowski, Kaori Sugihara ⁎
Department of physical chemistry, University of Geneva, 30 Quai Ernest Ansermet, Geneva, 1211, Switzerland

a r t i c l e i n f o a b s t r a c t

Article history: We performed a detailed deconvolution analysis of ATR-FTIR peaks of a common diacetylene, 10,12-
Received 8 February 2019 tricosadiynoic acid (TRCDA) during the polymerization and the blue-to-red transition. Based on the analysis
Received in revised form 10 April 2019 and the solvent dependence on the IR signals, we found that the triple peak from C`C stretching mode that
Accepted 14 April 2019
has been previously suspected as a consequence of Fermi resonance is rather associated with the macromolecular
Available online 16 April 2019
assembly of TRCDA. Besides these C`C triple peaks, we found that the background in the region increased during
Keywords:
the UV exposure due to the C`C signals from polymers. In addition, the anisotropic compression during poly-
Attenuated total reflectance Fourier transform merization was also detected, which supports the proposed interpretation of X-ray data reported previously.
infrared spectroscopy (ATR-FTIR) These results are the benefits from the deconvolution analysis.
Polydiacetylene (PDA) © 2019 Elsevier B.V. All rights reserved.

1. Introduction structural changes of PDA induced by stimuli such as light at different

wavelengths [21], pH [22], temperatures [23–26] and pressure pertur-
Diacetylenes are a class of molecules that contains a diacetylene bation [27]. Density functional theory [28,29] has also been used to bet-
moiety within their monomeric structure (left molecular scheme in ter understand the spectral changes. However, the deconvolution
Fig. 1). They can be polymerized into polydiacetylenes (PDA, right mo- analysis of diacetylene IR peaks has been understudied, thus the maxi-
lecular scheme in Fig. 1) [1–3] through the exposure to ultraviolet mum information may not have been extracted from IR spectroscopy
(UV) radiation, first synthesized in the 70s [4,5]. In an initial state, the in PDA systems.
polymer absorbs red light. This makes the PDA appear to be blue to In this work, we performed a detailed deconvolution analysis of
the naked eyes, therefore this state is defined as ‘blue state’. Further ATR-FTIR peaks of a common amphiphilic diacetylene, 10,12-
structural changes occur through UV irradiation, heat application, pH tricosadiynoic acid (TRCDA) during the polymerization and the blue-
change or peptide adsorption, which causes a spectral shift and changes to-red transition. Our ATR-FTIR setup is equipped with UV light source,
its color into red [6,7] (called ‘red state’ polymer) [8]. In addition, in the which realizes in-situ polymerization. The obtained IR spectra were
blue state the fluorescence pathway is forbidden, while it is allowed in compared with UV-VIS spectra for their detailed interpretation.
the red state. Due to this chromism, where both the color and the fluo-
rescent intensity change upon different stimulations, PDAs have gar- 2. Materials and methods
nered attentions in recent years for the applications in biosensors such
as the detection of peptides [9,10], viruses [11], ions [6], bacteria 2.1. Diacetylene monomer
[10,11], as well as other applications such as micropatterning [12,13],
and heat sensing [14]. 10,12-Tricosadiynoic acid (TRCDA, Lot. S30B033) was purchased from
After decades of studies, the structural change during the polymeri- Alfa Aesar, UK. It was stored as a powder in a freezer (T = −27 °C) to
zation and the mechanism of the blue-to-red transition are still contro- prevent spontaneous polymerization. Before the experiments they were
versial. Infrared (IR) spectroscopy has been frequently used for dissolved in chloroform (HPLC Grade, Fisher Chemical, USA) at a final
investigating the structure of PDAs due to its ability to keep track on concentration of 25 mg/ml and used within a week.
the bond change during the polymerization and the blue-to-red transi-
tions, besides Raman spectroscopy [15], carbon-13 nuclear magnetic 2.2. ATR-FTIR sample preparation
resonance (NMR) [16,17] and X-ray crystallography [18–20]. To date,
numerous Fourier-transform IR (FTIR) studies have focused on the Trapezoid ATR elements, made of zinc selenide (ZnSe, Korth Kristalle
GmbH, Germany) were cleaned with repeated wipes by chloroform and
⁎ Corresponding author. then dried with a stream of nitrogen (4.5 Purity Nitrogen, PanGas, Lot.
E-mail address: [email protected] (K. Sugihara). 756 311-10027020, CH) to remove the solvent. We chose ZnSe crystals

https://doi.org/10.1016/j.saa.2019.04.030
1386-1425/© 2019 Elsevier B.V. All rights reserved.
24 R.D. Ortuso et al. / Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy 219 (2019) 23–32

400 Homogenizer, Omni, USA) was applied for 15 min at 160 W with a
duty cycle of 20% to break up aggregates and to avoid excessive heating.
This suspension was further diluted to the final concentration at
8–50 mg/ml.

2.4. UV-VIS measurements

For UV-VIS spectroscopy, a V-670 (Jasco, USA) instrument was used

with a scan speed of 100 nm/min and with signal acquisition time of
0.4 s/nm. Systematic wavelength error is ±1.55 nm. The experiments
were repeated at least three times for confirming the reproducibility.
Fig. 1. Schematic representation of 10,12-tricosadiynoic acid (TRCDA) monomer and its These were analyzed by a home-made MATLAB® software
polymer form, polydiacetylene (PDA).
(MathWorks, Natick, USA) to process the large amount of data. Some
peak data sets were randomly chosen and were manually analyzed to
verify the consistency and correct functioning of the program.
due to their stability and inertness to UV-radiation as other materials
such as germanium can become electrically conductive and can inter-
fere with IR signals under UV light. After cleaning, they were stored 2.5. ATR-FTIR measurements
under Argon gas (5.0 Purity Argon, PanGas, Lot. 756 311-10658745,
CH) until use. 10 μl of TRCDA at a concentration of 25 mg/ml, dissolved A Vertex 80 V IR (Bruker Optics, USA) equipped with a potassium
in chloroform, were spin-coated (G3P-8 Spin Coater, SCS, Indianapolis bromide (KBr) beam splitter was used. The controller software was
USA) at 3000 rpm for 1 min 30 s on the clean zinc selenide trapezoid OPUS software (Version 7 Build 0.129). The light source was a 500 W
ATR crystal. solar simulator (LSH 302, LOT, Romanel-sur-Morges, Switzerland)
The height of the samples was up to 10 μm, estimated by taking a z- equipped with a UV band-pass filter (BG3, Lot. Y59203401, ITOS,
stack image with confocal microscopy (Fig. 2AB). Literature reports that Mainz, Germany). A custom-made sample holder was mounted to
TRCDA forms lamellar multilayers with the monolayer plane parallel to allow for ATR-FTIR measurements. Background scans were acquired
the substrate [30], yet in our samples atomic force microscopy (AFM) with a total of 1000 scans. Each TRCDA-PDA spectrum was acquired
topology captured a mixture of an amorphous-like area and micro- with a total of 250 scans with a resolution of 1 cm−1 with a range
crystal domains (Fig. 2C). The excess monomer outside of the UV- going from 400 to 4000 cm−1. Phase resolution of 4 units was used
irradiated area on the ATR cell was removed, so that TRCDA was depos- with a Mertz phase correlation and Blackman-Harris-3Term
ited only in the center region of the crystal. The samples were left over- apodization with 8 zero filling value [31]. In total, nine samples were
night in vacuum (20 mbar) to allow a complete evaporation of the measured, where the peak shifts were qualitatively similar. Here, we re-
organic solvent. Before measurements the ZnSe crystals were placed port only one set of representative data and its analysis. Each UV-dose-
in a home-made sample holder. The home-made sample holder enables dependence experiment is comprised of over 300 spectra in total, yet
the use of the identical substrate both for UV-VIS and ATR-FTIR mea- the deconvolution was performed by selecting a limited number of
surements without taking out the crystal each time. This allows the ac- spectra at UV area irradiation doses of 0.5, 1.0, 1.5, 2.0, 4.0, 6.1, 8.1,
curate comparison between UV-VIS and ATR-FTIR spectra, as ATR-FTIR 10.1, 20.3, 30.4, 40.6, 60.9, 80.2, 100.5, 120.8, 140.1, 160.4, 200.0,
is sensitive to the position of the crystal relative to the beam path. 235.7 J/cm2.
After the element chamber was sealed, nitrogen (5.0 Purity Nitrogen,
PanGas, Lot. 756 311-10426058, CH) was introduced for 30 min,
which ensures water vapor-free nitrogen atmosphere within the 2.6. IR transmission measurements
chamber.
The same Vertex 80 V IR (Bruker Optics, USA) was used for the IR
2.3. Preparation of PDA samples in different solvents transmission measurements (please see ATR-FTIR measurements sec-
tion for details). A custom transmission cell was mounted on the IR
0.5 ml of pentane, diethyl ether, chloroform or acetonitrile (all sol- beam path, composed by a two quartz windows and a 1-mm PTFE trap-
vents used were HPLC grade, Fisher Chemical, USA) was added to ezoid spacer interchange with a total chamber volume of 240 mm3. For
25 mg of TRCDA monomers. High power probe sonication (Sonic Ruptor the water sample the same setup was used with a spacer of 200 μm.

Fig. 2. TRCDA spin-coated on the ATR element imaged with A) bright field, B) confocal laser scanning and C) atomic force microscopy. A) A bright-field microscopy image with a 60× oil
immersion objective lens of a spin-coated sample after polymerization. B) A 3D reconstituted confocal laser scanning microscopy image of the sample in the area indicated with a dotted
red square in A. The vertical step size is 100 nm and a TRITC filter was used. C) Topology of the same sample imaged by atomic force microscopy in non-contact mode, where (α)
amorphous-like areas and (β) micro-crystal domains were observed.
 R.D. Ortuso et al. / Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy 219 (2019) 23–32 25

2.7. Data treatment the head-to-head configuration in .xyz format are available as
supporting information.
The data was exported into tab-separated-values (TSV) format via
the OPUS software. The deconvolution was performed by Fityk 1.3.1 3. Results and discussions
[32] with Gaussian fitting [33]. The number of fitting peaks was selected
such that the weighted residue between the original signal and the sum 3.1. Correlation of the polymer state (blue/red/degraded) with areal UV ir-
of the fitted peaks became b0.01. radiation doses

Our initial goal is to correlate the color of the sample and the UV
2.8. Quantum chemistry simulation of the IR spectra irradiation dose. We will use this result as a reference to interpret the
ATR-FTIR spectra later. To enable direct comparison between UV-VIS
Theoretical IR spectra were calculated within the harmonic ap- and ATR-FTIR spectra, exactly the same sample holder and UV source
proximation at the B3LYP/cc-pVDZ level of theory. For modelling were used during these experiments. Fig. 3A shows the UV-VIS absorp-
the polymer, propyl groups were used for the side chains. The ends tion spectra of TRCDA at different areal irradiation doses. Two character-
of the conjugated chains were saturated with a methyl group. The istic peaks, the blue state peak at around 650 nm and the red state peak
starting geometries for the monomer and the dimer were drawn at around 600 nm were observed, both of which shift during the UV
with Avogadro [34] and pre-optimized with a UFF [35] force field. irradiation (Fig. 3B). Note that both blue and the red peaks split into a
The starting geometries for the trimer and tetramer were obtained double peak structure [39], yet only the most intense peaks were
by duplication and subsequent translation of a monomeric moiety plotted in Fig. 3B. These transitions of the PDA electronic states have
in the dimer. A carboxylated heptamer model was obtained by car- been extensively studied previously [1,10,14,39]. The ratio between
boxylation of the propyl chain on one side of the model above. The the height of these blue and red peaks was plotted in Fig. 3C. Note that
optimization of this structure yields a hydrogen bond chain. Lastly, the extinction coefficients of blue and red PDA are in the same order of
a head-to-head hydrogen-bonded 2-monomer adduct was opti- magnitude (2.52 × 1010 M−1 cm−1 nm4 and 3.27 × 1010 M−1 cm−1 nm4
mized. All calculations were carried out in the gas phase, i.e. on an respectively) [40]. Ratio 100% suggests the point, where the amount of
isolated model molecule, neglecting the effect of the neighboring the blue and the red polymer are roughly equal. Ratio N 100% indicates
molecules in the condensed phase. The spectra reported are unscaled that the amount of the blue PDA is larger than that of the red PDA, while
[36,37]. The calculations were carried out with Gaussian09 [38]. The ratio b 100% suggests the opposite. From these results, we correlate the
optimized structure of the monomer and of the models used for state of the polymer (blue or red) with the irradiation dose as shown in
dimer, trimer, tetramer, carboxylated heptamer, and monomers in Fig. 3C: irradiation dose 0–90 J/cm2 is for the monomer to blue state

Fig. 3. UV-VIS spectra. A) UV-VIS spectra of TRCDA after different UV areal doses. B) Position of the red and the blue peak as a function of the UV doses. C) Blue to red ratio, calculated with
the height of the peaks. The vertical solid line highlights the point, in which the blue and the red polymers are at a 1:1 ratio (blue to red ratio 100%). D) Variation of the Area under the
absorption spectra between 480 nm and 710 nm over the amount of the UV dose. The vertical dashed line identifies the point, where 10% PDA was degraded.
26 R.D. Ortuso et al. / Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy 219 (2019) 23–32

polymerization (indicated as “blue state”), 90–170 J/cm2 is for the blue- Table 1
to-red transition (indicated as “red state”). Note that these assignments Spectral interpretation of ATR-FTIR signal in terms of the functional group.

are for the reference, and in reality the monomer, blue, and the red Bond Mode Type Region of Position in References
polymers are always expected to be mixed in the sample. When the interest molecule
samples are irradiated N170 J/cm2, the ratio further decreases [cm−1]

(Fig. 3C). To understand this region between 170 and 250 J/cm2, we CH3 Stretching Asymmetric 2970–2948 Termination tail [42–45]
plotted the area below the absorption spectra between 480 nm and CH2 Stretching Asymmetric 2948–2880 Tail
CH3 Stretching Symmetric 2877–2867 Termination tail
710 nm as a function of the irradiation dose, normalized by that of
CH2 Stretching Symmetric 2867–2830 Tail
the monomer (0 J/cm 2 irradiation) in Fig. 3D. The area under the C≡C Stretching – 1980–2275 Monomer tail or
spectra indicates the total amount of the blue and the red polymer conjugated pol.
in the sample as monomers or degraded polymers that lost the C=O Stretching – 1800–1600 Head
conjugated backbone present no clear absorption peaks [41]. The C=C Stretching – 1580–1500 Conjugated pol.
CH2 In-plane – 1476–1453 Tail
initial increase, followed by a plateau until around 170 J/cm2, is in bending
good agreement with the assignment of the polymer states defined
by the peak ratio in Fig. 3C, because during the monomer to blue
state polymerization the amount of the conjugated polymer should
increase, while during the blue-to-red transition the total amount 3.3. The triple (C`C) and the double (C=C) carbon-carbon bonds reveal
of the blue and the red polymers should stay constant. After the polymerization process
170 J/cm2, the area decreases rapidly, which implies degradation of
the polymer. At 250 J/cm 2, around 70% of PDAs were degraded, As the scheme in Fig. 1 shows, an expected major change in the
evidenced by the loss of the area by 70%. For the following, these chemical structure during the polymerization is the reduction of the tri-
assignments of “blue (monomer-to-blue state)”, “red (blue-to- ple carbon carbon bond (C`C), accompanied by the formation of a dou-
red)”, “degraded states” will be used to interpret the ATR-FTIR data. ble carbon-carbon bond (C=C), which is initially absent in monomers.
In the monomer state, we detected multiple peaks around the triple
carbon-carbon bond (C`C) region, including the characteristic triple
3.2. ATR-FTIR spectra were obtained and the peaks were assigned peaks in TRCDA that have been reported before [28] (highlighted by vi-
olet, green and yellow deconvolutions in Fig. 5A.I). Note that the rest of
Next, we obtained the ATR-FTIR spectra of TRCDA during the UV the deconvoluted peaks are shown in grey. Previously, double peaks in
irradiation (Fig. 4). The assigned peaks are summarized in Table 1. the C`C region in diacetylene monomers have been interpreted as a
Overall the IR spectra change during the UV exposure is rather sub- consequence of Fermi resonance [28], but the origin of the third peak
tle. Nevertheless, these zoom-out spectra are shown to confirm e.g. in TRCDA is left elusive. First, we thought that these are signals from
the absence of signals from free OH group in the 3500 cm−1 region, spontaneously-polymerized short-chain polymers mixed in monomers
which suggests that most of the carboxyl head groups are hydrogen because C_C signals indicate the presence of polymer as we will ex-
bonded [46,47]. In the following, we will perform the detailed plain later. However, this idea was rejected as the height ratio of these
deconvolution analysis for C`C (1980–2275 cm −1), C_C three peaks is almost identical for different batches and storage time
(1580–1500 cm−1), C_O stretching (1800–1600 cm−1), CH2 sym- of monomers (Fig. S1), where it is unlikely that the population of differ-
metric stretching (3600–2380 cm −1 ) and in-plane CH2 bending ent short-chain polymers are exactly the same. These triple peaks seem
(1490–1310 cm−1) peaks. to be sensitive to solvent (Fig. 5BC, where the possible assignment of vi-
olet, green and yellow peaks and their peak position as a function of the
solvent polarity are shown). Amphiphilic molecules self-assemble into
different macromolecular structures in solvent with different polarities
[49]. For example, the intermediate polarity of chloroform (0.26) allows
amphiphilic molecules to be dispersed as a monomer, whereas an ex-
treme polar (e.g. water: 1) or non-polar (e.g. pentane: 0.01) solvent in-
duce the assembly of bilayers/micelles or inverted bilayers/micelles,
respectively. The fact that monomer C`C signal has a relatively simple
peak in chloroform, whereas it splits into multiple peaks in higher or
lower polar solvent suggests that these multiple peaks come from vari-
ous packing environments of the monomer. The deconvolution analysis
shows that the areas below these triple peaks all decrease during the UV
exposure as the population of the triple bonds in monomers diminishes
(Fig. 5A.II) and more polymer is formed. The slight positive peak shifts
during the monomer-to-blue polymerization (Fig. 5A.III) imply the
compression of the diacetylene upon the conformational change during
the polymerization. In contrast, the sum of the rest of the peaks within
the region (1980–2275 cm−1, indicated as grey deconvoluted peaks) in-
creased during the UV exposure (the grey plot in Fig. 5A.II). This back-
ground increase probably originates from many different C`C peak
signals from polymers with different chain lengths. IR peak simulation
from short polymer chains appear around in this region with different
peak shifts (Fig. S2), supporting this idea. In addition, their larger con-
formational freedom such as slight torsions or kinking of the polymer
Fig. 4. ATR-FTIR spectra of TRCDA at 0 J/cm2 (black), blue (blue), red (red), and degraded backbone could have contributed in splitting the peaks.
(grey) states. The blank ATR-FTIR ZnSe element was used as reference spectra and the
The peak from C_C was detected even before the UV irradiation
baseline was subtracted. All the peaks that are identified and will be analyzed later are
indicated by wavenumbers. Note that C`C peaks (2181, 2167, 2139 cm−1) are not (the deconvoluted light blue peak in 0 J/cm2 in Fig. 6A.I). This indicates
visible in the figure since their intensities are small. See the zoom-in Fig. 5 for the detail. the presence of polymers even before the active UV irradiation. In fact it
 R.D. Ortuso et al. / Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy 219 (2019) 23–32 27

Fig. 5. C`C stretching peaks. A.I) ATR-FTIR spectra for C`C stretching at different UV areal irradiation doses, where the results from the deconvolution are superposed. The regions within
the two vertical dashed lines were used for the deconvolution. The characteristic triple peaks from C`C stretching that have been reported before are highlighted by violet, green and
yellow. A.II) The normalized area underneath the peaks and A.III) peak position vs areal irradiation doses. B) The characteristic triple peaks changed their intensities and positions,
depending on the solvent environments.
28 R.D. Ortuso et al. / Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy 219 (2019) 23–32

Fig. 6. C_C and C_O stretching modes. A.I) ATR-FTIR spectra for C_C and C_O stretching at different UV areal irradiation doses, where the results from the deconvolution are
superposed. A.II) The normalized area underneath the peaks and A.III) peak position vs areal irradiation doses for characteristic peaks at 1539, 1692, 1698, 1736 cm−1. B) Simulated IR
spectra from C_O stretching mode, where hydrogen bonds exist intra or inter layers.

is well-known that diacetylene self-polymerizes when stored in chloro- 3.4. C_O stretching mode reveals different types of hydrogen bonds at the
form [50]. As the sample is irradiated with UV, the area under the C_C headgroup
peak increases only by around three folds during the monomer-to-blue
polymerization (Fig. 6A.II), indicating that the amount of the double The diacetylene monomer used in this work, TRCDA, has a carboxyl
carbon-carbon bond tripled. The area keeps a plateau during the red headgroup. IR peaks from carbon-oxygen double bond stretching (C=
state (Fig. 6A.II), which is in agreement with the fact that little or no O) are commonly employed to study the hydrogen bonding of the
bond change is expected during the blue-to-red polymer conformation headgroup [51]. In our samples, a clear C_O stretching peak was ob-
change. Note that even though the polymerization reached the satura- served as expected (Fig. 6A.I). The deconvolution revealed three main
tion, some monomers may have still remained in the samples peaks in the monomer state TRCDA (violet, green and yellow) and
unpolymerized because we observed some monomers in amorphous broad background peaks (grey) that appear upon UV exposure
structures that are not in a favorable alignment for polymerization (Fig. 6A.I). The origin of these multiple peaks has been previously ex-
(Fig. 2C). The slight decrease during the degradation can be due to the plained by the number of the hydrogen bonds per C_O, where the
opening of the double bonds and formation of degraded species. The more hydrogen bonds are present, the lower the wavenumber is
stability of the peak position (Fig. 6A.III) indicates that the double [24,25,47]. In our samples, a lack of the characteristic peak for the free
carbon-carbon bonds (C=C) are not significantly influenced by the en- OH group around 3500 cm−1 (Fig. 4) suggests that most of the carboxyl
vironment during these processes. head groups are hydrogen bonded [46,47]. Another interpretation
 R.D. Ortuso et al. / Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy 219 (2019) 23–32 29

hinges on the conformation of the hydrogen bonds rather than on their [24,25,47,52]. The effect of solvents with different polarity on the hydro-
number such as inter- or intra-layer bonding. Simulation shows that the gen bonds between carboxyl head groups has also been investigated
presence of intra- (simulated with a tetramer and a heptamer, where [53,54]. When lipids were exposed to a more polar environment the
hydrogen bonds are assumed in parallel to the conjugation) or inter- C_O stretching shifts towards lower wavenumbers [53,54]. This occurs
layer hydrogen bonds (simulated with two monomers, where a head- due to the involvement of the lone pair in the non-covalent interaction,
to-head hydrogen bond is assumed) causes splitting in the C_O which withdraws electron density from the C_O bond, weakens it, and
stretching peaks (Fig. 6B). This implicates that the simulation does not consequently lowers the characteristic resonance frequency.
reject the second explanation.
All three peaks present a slight areal decrease upon UV exposure (vi- 3.5. CH2 in-plane bending and CH2 symmetric stretching both indicate an
olet, green and yellow in Fig. 6A.II), which suggest the breaking of the hy- anisotropic packing
drogen bonds and the declined interactions between head groups during
the UV exposure. Among these three peaks, the 1692 cm−1 peak (yellow) The information on the CH2 side chains can be obtained by analyzing
shifted its position slightly in the initial UV irradiation and leveled off im- the in-plane bending of CH2 (Fig. 7A) since it is sensitive to interdigita-
mediately during the blue state (Fig. 6A.III). In contrast, both 1698 cm−1 tion changes, hence the packing, of alkyl chains. Van der Waals forces
(green) and 1736 cm−1 (violet) peaks kept shifting towards higher are mainly responsible for influencing this type of movement. The
wavenumbers also during the red state. This is because the conforma- deconvolution of this peak revealed two components (Fig. 7A.I). The
tional changes during the polymerization and the blue-to-red transition peak with a lower wavenumber (1463 cm−1 in yellow) slightly de-
are different, where different types of hydrogen bonds are broken either creases its intensity during the UV exposure, while the one with a higher
during the polymerization or blue-to-red transition or both. These results wavenumber (1465 cm−1 in violet) initially increases, followed by a
are consistent with the picture coming from the alkyl chain peaks (CH2 slight decrease. This cannot be explained by uniform packing or expan-
stretching and CH2 in-plane bending in Figs. 7, 8) and the previous reports sion, because if the sample were compacting/expanding in all directions
[18,19,24,46,47], where diacetylene monomers form ordered hexagonal we would expect a monotonous decrease/increase in both components.
lattice, while the polymerization distorts the lattice and induce a higher Previously, the deconvoluted double peaks from the CH2 in-plane bend-
disorder as will be discussed later. Previously a similar change in the ing signal has been interpreted as a consequence of the interactions of
C_O intensity or its peak position has been observed with other amphi- alkyl chains in different directions [55]. In their work, high and the
philic molecules during the variation of temperature [24,25,47,52]. As am- low wavelength peaks have been associated to the short and the long
phiphilic molecules undergo the phase transition induced by lattice of the fundamental cells respectively [55], while the difference
temperature, the reduction of the structural order caused a decrease in between these wavenumbers has been linked to the lattice angle of
the C_O stretching signal and a shift in the wavenumber towards higher the two conformations [55,56]. Our result implies that there is a direc-
positions, indicating a higher degree of freedom of the C_O group tion in the diacetylene lattice that is rather slightly expanding (un-

Fig. 7. CH2 in-plane bending mode. A.I) ATR-FTIR spectra for CH2 in-plane bending mode at different UV areal irradiation doses. A.II) The area underneath the peaks vs UV areal irradiation
doses and A.III) peak position vs areal irradiation doses. AI) ATR-FTIR spectra, II) the analysis of the area underneath the peak vs UV irradiation energies, where arrows indicate irradiation
energies at which the deconvolution was studied, and III) the peak shift vs UV irradiation energies are shown. The region within the two vertical dashed lines in A.I indicates the
wavenumber areas that were interpreted as one peak. B) Overlaying plot of the original spectra and the sum of the deconvoluted spectra, where the good overlap ensures the
successful deconvolution. C) Deconvoluted spectra of CH2 in-plane bending ATR-FTIR signal at 0 J/cm2 (in black), blue polymer (40.6 J/cm2 in blue), and red polymer (162.5 J/cm2 in red).
30 R.D. Ortuso et al. / Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy 219 (2019) 23–32

Fig. 8. CH2 symmetric stretching mode. A.I) ATR-FTIR spectra for CH2 symmetric stretching mode at different UV areal irradiation doses. A.II) The area underneath the peaks vs UV areal
irradiation doses and A.III) peak position vs areal irradiation doses.

packing) during the initial state of the polymerization among other di- modes results in the decrease of the peak area. In the present data, one
rections that are contracting (packing). This finding is interesting be- of these two peaks increased the peak area during the initial polymeriza-
cause such a lattice deformation of PDA during polymerization has tion (2849 cm−1 in violet in Fig. 8A.II), followed by a decrease, whereas
been monitored previously by gradient incidence X-ray electron diffrac- the other (2846 cm−1 in yellow in Fig. 8A.II) kept decreasing upon the
tion (GIXD) experiments, where a lattice constant in one direction in- UV exposure. The behavior of these two peaks is in agreement with the
creases and the other direction decreases during the monomer-to- anisotropic compression observed in CH2 in-plane bending mode.
blue state polymerization [19]. This detection of an additional expan- In contrast, the positions of both peaks shifted towards higher
sion of the TRCDA assemblies at the initial state of the polymerization wavenumbers monotonously upon UV exposure (Fig. 8A.III), which in-
is a benefit from the deconvolution analysis. Typically X-ray crystallog- dicates the decrease in the degree of the alkyl chain order [19]. Previ-
raphy or theoretical works show that the area per molecule declines by ously, during the phase transition from solid to liquid crystal, a total
around 1% during the polymerization (monomer-to-blue polymeriza- peak shift of around 5 cm−1 has been observed [60]. In our case, the
tion) [19] and it does by 2–21% [18,19] during the blue-to-red transition. shifts are less pronounced (1–1.5 cm−1, Fig. 8A.III) for both peaks, and
The shrinkage of PDAs upon polymerization has been observed also by they took place mainly during the polymerization (monomer-to blue
atomic force microscopy [57,58] (AFM) and scanning tunneling micros- state). Gradient incidence X-ray electron diffraction (GIXD) experi-
copy [59] (STM), thus the compression is a well-recognized phenomena ments have shown that the diacetylene monomers assemble into a hex-
but the expansion has been reported much less. For the peak position, a agonal lattice, which deforms and breaks the symmetry during the
slight shift towards a higher wavenumber was observed for both peaks, polymerization and the blue-to-red transition [19,60,64,67]. The slight
indicating packing [60]. peak shifts in our experiments probably also detected this deformation
To further study the effects of the polymerization on the alkyl chain of the lattice and the associated disorder of the alkyl chains.
packing, the signals arising from the CH2 symmetric stretching vibra- By combining the information that we obtained from the backbone
tions [61,62] were also analyzed (Fig. 8A.II). These wavenumber regions (Figs. 5, 6), alkyl side chains (Figs. 7, 8), and the headgroup (Fig. 6),
are known to be correlated with the conformational order of the alkyl we find a following global view. Upon UV exposure the polymerization
tails [60,62–64], thus have been studied extensively to clarify the of the backbone induces the anisotropic packing in the side chains, de-
chain conformation and the lattice structure [60]. Note that the corre- forms the lattice, and increases the disorder, which breaks the hydrogen
sponding asymmetric CH2 stretching vibration was also observed but bonds at the headgroup. While the backbones and the alkyl chains are
discarded from the analysis, because they are known to be difficult to in- being packed, the compression of the headgroup was not observed.
terpret due to the influences from Fermi resonances [64–66]. This is possible because the backbone and the headgroup are connected
The deconvolution revealed two main peaks (violet and yellow spec- with flexible single carbon-carbon bonds in TRCDA, enabling the head
tra in Fig. 8A.I) apart from the broad background peaks (grey spectra) group to escape from the compression by shifting their position out-
that overlap with CH2 asymmetric stretching mode. The area under the of-plane from the conjugated backbone. This may also be a part of the
absorption curve in CH2 symmetric stretching reflects the inter-alkyl reason why we and other researchers detected the slight PDA expansion
chain interactions, thus also packing [64]. When the alkyl tails are in a certain direction due to the steric hindrance that comes from the
more compact (packing), the restricted movement of these vibrational head groups.
 R.D. Ortuso et al. / Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy 219 (2019) 23–32 31

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