Tuning of aggregation and film self-assembly of monomethincyanine dyes through variation of their monomer structure
Formation of condensed films and solution aggregates of four different monomethincyanine dyes has been studied using optical absorption spectroscopy and simulation methods, depending on variation of the dye monomer structure. The structure of the molecular dimer as a basic unit for the formation of...
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| Опубліковано в: : | Semiconductor Physics Quantum Electronics & Optoelectronics |
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Інститут фізики напівпровідників імені В.Є. Лашкарьова НАН України
2019
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| Цитувати: | Tuning of aggregation and film self-assembly of monomethincyanine dyes through variation of their monomer structure / M.M. Sieryk, O.P. Dimitriev // Semiconductor Physics Quantum Electronics & Optoelectronics. — 2019. — Т. 22, № 1. — С. 53-59. — Бібліогр.: 16 назв. — англ. |
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Digital Library of Periodicals of National Academy of Sciences of Ukraine| _version_ | 1860480565248000000 |
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| author | Sieryk, M.M. Dimitriev, O.P. |
| author_facet | Sieryk, M.M. Dimitriev, O.P. |
| citation_txt | Tuning of aggregation and film self-assembly of monomethincyanine dyes through variation of their monomer structure / M.M. Sieryk, O.P. Dimitriev // Semiconductor Physics Quantum Electronics & Optoelectronics. — 2019. — Т. 22, № 1. — С. 53-59. — Бібліогр.: 16 назв. — англ. |
| collection | DSpace DC |
| container_title | Semiconductor Physics Quantum Electronics & Optoelectronics |
| description | Formation of condensed films and solution aggregates of four different monomethincyanine dyes has been studied using optical absorption spectroscopy and simulation methods, depending on variation of the dye monomer structure. The structure of the molecular dimer as a basic unit for the formation of the condensed state was found to be largely dependent on heteroatoms in the dye structure and the presence of end hydrocarbon groups. The above factors mainly determine the mutual position of molecules in the dimer. It has been found that mutual orientation, intermolecular distance, and overlap of the adjacent molecules are the major factors influencing absorption spectra of dye aggregates. The dimer geometry that plays the primary role in film nucleation, however, has been shown to undergo changes depending on the temperature conditions or film thickness.
|
| first_indexed | 2026-03-23T19:02:11Z |
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ISSN 1560-8034, 1605-6582 (On-line), SPQEO, 2019. V. 22, N 1. P. 53-59.
© 2019, V. Lashkaryov Institute of Semiconductor Physics, National Academy of Sciences of Ukraine
53
Hetero- and low-dimensional structures
Tuned aggregation and film self-assembly of monomethincyanine dyes
through variation of their monomer structure
M.M. Sieryk, O.P. Dimitriev
V. Lashkaryov Institute of Semiconductor Physics, NAS of Ukraine
41, prospect Nauky, 03680 Kyiv, Ukraine
E-mail: serikmykola@gmail.com
Abstract. Formation of condensed films and solution aggregates of four different
monomethincyanine dyes have been studied using optical absorption spectroscopy and
simulation methods, depending on variation of the dye monomer structure. The structure of
molecular dimer as a basic unit for formation of the condensed state was found to be largely
dependent on heteroatoms in the dye structure and the presence of end hydrocarbon groups.
The above factors mainly determine the mutual position of molecules in the dimer. It has
been found that mutual orientation, intermolecular distance and overlap of the adjacent
molecules are the major factors influencing absorption spectra of dye aggregates. The dimer
geometry that plays the primary role in film nucleation, however, has been shown to
undergo changes depending on the temperature conditions or film thickness.
Keywords: self-assembly, aggregate, monomethincyanine dyes, absorption spectrum.
doi: https://doi.org/10.15407/spqeo22.01.53
PACS 78.40.Me, 81.16.Dn
Manuscript received 11.01.19; revised version received 29.01.19; accepted for publication
20.02.19; published online 30.03.19.
1. Introduction
Self-assembly of molecular systems is driven mostly by
competition of molecule-molecule and molecule-
environment (solvent, substrate, etc.) interactions [1, 2].
Since the above interactions are normally weak and
dominating by weak electrostatic and van der Waals
forces, the long-range order of the self-assembled system
does not normally persist, while the short-range order can
undergo significant variations providing rather different
geometry of molecular pairs in dimmers that play the role
of elementary units to construct the bulk structure [3].
The rate of self-assembly is another factor that
influences the final structure of a self-assembled system.
The film samples from solution were formed relatively
slowly, which is controlled by the rate of solvent
evaporation. The films prepared using vacuum
evaporation are formed faster through immediate sticking
of molecules to the substrate, where the molecules
possess rather slow mobility as compared to that in
solution, resulting in more loose structure obtained.
One of the main factors that defines the
intermolecular interaction is the chemical structure of
molecule, which can be tuned to drive the structure of the
condensed film overall and to change its physical
properties, respectively. Monomethincyanine dyes
belong to polymethine dyes serving as convenient model
objects that allow one to understand how slight variation
in the molecular structure can influence formation of the
aggregate or bulk structure [4-7]. These dyes have
relatively short length and are stable upon thermal
evaporation in vacuum [8]. They can be found in
different optoelectronic applications, such as optical
switching [9], fluorescent probes [10], photographic
imaging [11], etc.
In this work, we study aggregate formation of
monomethincyanine bases with unsymmetrical neutral
linear structure containing donor and acceptor terminal
groups, which can be considered as neutral derivatives
produced from the corresponding cationic cyanines with
the same π-elecron system. Similarly to other
polymethine dyes, monomethincyanine bases have highly
polarizable collective system of π-electrons and possess
high molar absorption coefficient and high
hyperpolarizabilities. On the other hand, these dyes,
owing to their unsymmetrical structure, have large dipole
moments in both ground and excited states [5]. We
demonstrate that a slight variation in the dye structure
possessing the same chromophore nuclei can lead to
significant changes in formation of their condensed films.
SPQEO, 2019. V. 22, N 1. P. 53-59.
Sieryk M.M., Dimitriev O.P. Tuned aggregation and film self-assembly of monomethincyanine dyes …
54
2. Experimental
Four types of intraionic (monometine) dyes (bases of
asymmetric monometincyanine derivatives of
benzo[c, d]indole) were investigated (Fig. 1). The dyes
were synthesized at Institute of Organic Chemistry,
National Academy of Sciences of Ukraine as described
elsewhere [5]. Monomer solutions of these compounds
were prepared by dissolving the dye molecules in
dioxane. The stock solution had the concentration of
10–3 M, but optical absorption spectra were recorded for
the diluted (10–5 M) solutions. Dye aggregation was
provided by addition of a small amount (1 vol.%) of the
dioxane stock solution to the distilled water, where the
compounds are not soluble. The spectra of solutions were
measured using the Avantes-2048 spectrophotometer and
corrected for the pure solvent.
Films were deposited using the VUP-5 vacuum
chamber equipped with the optical spectrometer Polytec
to control the spectral changes in-situ. Compounds were
evaporated at the pressure of 10–3 Pa by using resistive
heated silica crucible. Thin films of dyes were fabricated
at the deposition rate of 0.1…1.6 Е/s onto the cleaned
and annealed glass substrates.
Morphology of prepared specimens was
investigated with the AFM microscope NanoScope IIIa
(Digital Instruments, USA). Molecular simulation was
performed with Gaussian 09 and Materials Studio 8.0
(Forcite Module) software by using the density
functional method (DFT/B3LYP 6-31+(d,p)) and the
method of molecular dynamics (MD).
3. Results and discussion
3.1. Self-assembly of Py
The structure of Py molecule (Fig. 1) was found to be
ideally flat, with a zero torsional angle between the
benzo[c, d]indole and pyridine units as described by the
simulation results (Table 1). The flat structure of the
monomer facilitates formation of almost ideal molecular
stacks when forming a dimer (Fig. 2a, Table 1). This
stacking or H-aggregate formation should be identified
through blue shift in the absorption spectra [12, 13].
However, it was found an insignificant blue shift of the
dimer spectrum relatively the monomer one, by only
~200 cm–1 (Fig. 2b). Moreover, formation of films did
not show any clear spectral shift of the absorption band.
Instead, the band was broadened, indicating significant
disorder in the film structure. The microscopic image
confirmed that the film structure had amorphous
character, since no formation with a regular shape was
found (Fig. 2c).
The contradiction between ability of Py molecules
to form ideal short-order within a dimer and failure to
form the long-range order can be explained by relatively
large distance between the molecules (Table 1). Speci-
fically, the equilibrium distance between the molecules
with no hydrogen bonding should be about 3.5 Å [14],
while a 3.65 Å Py–Py distance has been found in the
dimer. This large distance leads to more relative freedom
of molecules separated by this distance and, therefore, to
high disorder in the condensed state, respectively.
2404 (Py)
2400 (Qu-Me)
2403 (BT)
2406 (In)
Fig. 1. Chemical structure of the compounds used.
N N
CH3
N N
CH3
N S
N
CH3
N N
H3C
H3C CH3
SPQEO, 2019. V. 22, N 1. P. 53-59.
Sieryk M.M., Dimitriev O.P. Tuned aggregation and film self-assembly of monomethincyanine dyes …
55
3.2. Self-assembly of Qu-Me
The structure of Qu-Me molecule (Fig. 1) is somewhat
different from that of Py by the presence of pyridine at
the quinoline unit only. However, this change leads to
significant difference in the aggregate behavior. First, it
was found that the dimer of Qu-Me is also ideally flat,
with the zero torsional angle between the
benzo[c, d]indole and quinoline nuclei as described by
the simulation results (Table 2), however, the
intermolecular distance is notably shorter and close to
3.2 Å. The flat structure of the monomer implies
formation of almost ideal molecular stacks in the dimer
as well (Fig. 3a, Table 2). And this stacking or H-
aggregate formation is really identified through blue shift
in the absorption spectra (Fig. 3b). Specifically, the
monomer absorption in the solution shows an electronic
0-0 transition at ~15870 cm–1 accompanied by vibronic
transitions separated by ~1200 cm–1, whereas the
absorption spectrum of the dimer is blue shifted in
respect to the monomer absorption by ~2000 cm–1, which
indicates that the molecules tend to form H-aggregates.
16000 18000 20000 22000 24000
0.000
0.002
0.004
0.006
0.008
0.010
0.012
3
3
2
Wavenumber, cm-1
A
bs
or
ba
nc
e,
a
.u
. 1
Fig. 2. (a) Simulated structure of Py monomer and dimer, (b) electronic absorption spectra of monomer in dioxane solution (blue, 1),
dimer in aqueous solution (red, 2) and evaporated film with increasing thickness (grey, 3), (c) typical AFM image of the film
surface.
Table 1. Parameters of Py monomer and dimer obtained as a result of simulation.
Dimer
Physical quantity Monomer
Molecule 1 Molecule 2
Torsion angle 0 0 0
Dipole moment 1.62 1.51 1.51
Angle between dipole moments of
molecules (cos α)
150°(–0.86)
Dipole moment of dimer 0.8
Distance between molecules (Å) 3.65
a
b c
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Sieryk M.M., Dimitriev O.P. Tuned aggregation and film self-assembly of monomethincyanine dyes …
56
However, the Qu-Me film growth on the glass
substrate demonstrates a totally different trend. The film
spectrum is red shifted in respect to the monomer
absorption, which corresponds to formation of J-
aggregates in the condensed film [14]. The marginal
signs of H-aggregates can be seen only as a broadening
from the high-energy side of the film spectrum (Fig. 3b).
The observed difference between the aggregate structures
in solutions and films can be explained by different dye-
solvent and dye-substrate interactions. Although in both
cases the dye environment is hydrophilic, in the case of
solution the dimers are isolated in a disordered
hydrophilic environment, while in the condensed film the
molecules tend to be arranged in more extended
aggregates, which structure can be dictated by the
crystalline order. Indeed, the AFM image of the film
(Fig. 3c) indicates the presence of species with quasi-
regular shapes, which is characteristic of crystallite
formation. Similar result was obtained in ref. [15]. Thus,
the flat molecular structure of Qu-Me allows the
molecules to approach relatively small distance to each
other (Table 1) and leads to formation of two types of
aggregates, either H- or J-type. It is interesting to note
that J-aggregates can be transformed to H-aggregates
through film relaxation (green curve 4 in Fig. 3b).
3.3. Self-assembly of BT
The equilibrium structure of BT molecule (Fig. 1) is not
ideally flat and displays a certain torsion angle between
the donor and acceptor units (Table 3). Nevertheless,
14000 16000 18000 20000 22000 24000
0.00
0.01
0.02
0.03
0.04
0.05
0.06
0.07
0.08
3
3
3
3
3
4
A
bs
or
ba
nc
e,
a
.u
.
Wavenumber, cm-1
1
2
3
200nm
Fig. 3. (a) Simulated structure of Qu-Me monomer and dimer, (b) electronic absorption spectra of monomer in dioxane solution
(blue, 1), dimer in aqueous solution (red, 2) and evaporated film which was monitored during growth in-situ (grey, 3) and then
relaxed for 10 minutes after evaporation (green, 4), (c) typical AFM image of the film surface.
Table 2. Parameters of Qu-Me monomer and dimer obtained as a result of simulation.
Dimer
Physical quantity Monomer
Molecule 1 Molecule 2
Torsion angle 180° 178° 178°
Dipole moment 2.24 1.15 1.16
Angle between dipole moments of
molecules (cos α)
175°(–0.99)
Dipole moment of dimer 0.09
Distance between molecules (Å) 3.2
a
b c
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Sieryk M.M., Dimitriev O.P. Tuned aggregation and film self-assembly of monomethincyanine dyes …
57
according to the simulation results, the intermolecular
distance in the BT dimer is relatively small, i.e., 3.35 Å,
which leads to the significant difference in the dimer
spectrum as compared to that of monomer one (Fig. 4).
Specifically, the spectral features of the BT dimer were
characteristic of H-aggregate. However, the BT film
again demonstrated a totally different trend, similar to
that observed in Qu-Me films, i.e., the film spectrum was
red-shifted in respect to the monomer absorption, which
corresponds to formation of J-aggregates in the
condensed film. This difference between the aggregate
structures in solutions and films can be again explained
by different dye-solvent and dye-substrate interactions,
where in the condensed film the molecules tend to be
arranged in more extended aggregates, which structure is
dictated by the crystalline order. The AFM image of the
film (Fig. 4c) indicated the structure composed of
features of several hundreds of nanometers in size,
suggesting formation of crystallites. That means that the
molecular structure of BT allows the molecules to form
two types of aggregates, either H- or J-type, similar to
those of Qu-Me molecules above.
3.4. Self-assembly of In
The structure of the In molecule is different from that of
BT by replacement of the sulfur atom in BT
chromophore with the carbon atom, to which two
additional methyl groups are attached (Fig. 1). The
presence of additional side groups may provide a certain
14000 16000 18000 20000 22000 24000
0.00
0.01
0.02
0.03
0.04
0.05
0.06
0.07
3
3
3
3
3
3
3
1
Wavenumber, cm-1
A
bs
or
ba
nc
e,
a
.u
.
2
2.0µm
Fig. 4. (a) Simulated structure of BT monomer and dimer, (b) electronic absorption spectra of monomer in dioxane solution (blue,
1), dimer in aqueous solution (red, 2) and evaporated film monitored during growth in-situ (grey, 3), (c) typical AFM image of the
film surface.
Table 3. Parameters of BT monomer and dimer obtained using simulation.
Dimer
Physical quantity Monomer
Molecule 1 Molecule 2
Torsion angle –11.5° –15.5° –12.2°
Dipole moment 3.41 3.19 3.41
Angle between dipole moments of
molecules (cos α)
122°(–0.54)
Dipole moment of dimer 2.95
Distance between molecules (Å) 3.35
a
b
c
c
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Sieryk M.M., Dimitriev O.P. Tuned aggregation and film self-assembly of monomethincyanine dyes …
58
hindrance between approaching molecules, which can
affect formation of the tight dimer structure. Simulation
showed that the intermolecular distance in the In dimer is
relatively large, being 3.9 Å, and the overlap of
molecules is poor (Fig. 5a, Table 4). As a result, the
dimer spectrum was only slightly blue-shifted in respect
to the monomer absorption, and films also demonstrated
broadened and structureless spectra (Fig. 5b), indicating
that the film structure contains high disorder. It should be
noted that the above results are similar to those of Py,
although the structure of the Py and In molecules are
quite different.
4. Conclusions
In summary, experimental and simulation results of the
aggregate formation of four different monomethin-
cyanine dyes allowed us to derive the major factors
responsible for the structural changes both in elementary
aggregates, i.e., dimers, and in extended condensed films
of these compounds as well. The major parameter is the
molecular structure that, dependent on its specific, allows
the molecules to approach by different distance and to
form different extent of overlap due to the balance of the
repulsive and attractive forces, respectively. The
14000 16000 18000 20000 22000 24000
0.00
0.01
0.02
0.03
0.04
0.05
0.06
0.07
0.08
0.09
3
3
3
3
2
Wavenumber, cm-1
A
bs
or
ba
nc
e,
a
.u
.
1
Fig. 5. (a) Simulated structure of In monomer and dimer, (b) electronic absorption spectra of monomer in dioxane solution (blue, 1),
dimer in aqueous solution (red, 2) and evaporated film monitored during growth in-situ (grey, 3).
Table 4. Parameters of In monomer and dimer obtained as a result of simulation.
Dimer
Physical quantity Monomer
Molecule 1 Molecule 2
Torsion angle 165.3° 170.5° 172.8°
Dipole moment 2.49 2.24 2.29
Angle between dipole moments of
molecules (cos α)
40°(0.76)
Dipole moment of dimer 4.3
Distance between molecules (Å) 3.9
a
b
SPQEO, 2019. V. 22, N 1. P. 53-59.
Sieryk M.M., Dimitriev O.P. Tuned aggregation and film self-assembly of monomethincyanine dyes …
59
intermolecular distance and overlap then defines the
extent of intermolecular interaction and influences on
electronic excitation in the aggregate. Thus, the tentative
aggregate structure can be inferred as based on electronic
absorption spectra of the species. However, it should be
noted that although the main understanding on relation
between elementary H- and J-aggregate structures and
their absorption spectra was reached long ago [16], still
there is a plenty of room to explain specific aggregate
behavior of complex molecules like the studied ones.
Particularly, similar stacking of the molecules into the
dimer structure was shown to produce different
absorption spectra, depending on the mutual overlap and
intermolecular distance of the molecules.
Acknowledgements
We thank to Dr Yu. Slominskii for dyes granting,
Dr P. Lytvyn for AFM studies and Dr K. Grytsenko for
useful comments.
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Authors and CV
Mykola M. Sieryk, Researcher at the
V. Lashkaryov Institute of Semi-
conductor Physics, NAS of Ukraine.
Authored over 6 publication and 2
patents. The area of his scientific
interests is optical properties and self-
organization of molecular thin films.
Oleg P. Dimitriev, Senior Research
Fellow at the V. Lashkaryov Institute
of Semiconductor Physics, NAS of
Ukraine. The author of over 100
publications, including 6 patents and
2 books. The area of his scientific
interests includes material science of
organic and hybrid heterostructures
and photophysics of conductive
polymers and dyes.
|
| id | nasplib_isofts_kiev_ua-123456789-215427 |
| institution | Digital Library of Periodicals of National Academy of Sciences of Ukraine |
| issn | 1560-8034 |
| language | English |
| last_indexed | 2026-03-23T19:02:11Z |
| publishDate | 2019 |
| publisher | Інститут фізики напівпровідників імені В.Є. Лашкарьова НАН України |
| record_format | dspace |
| spelling | Sieryk, M.M. Dimitriev, O.P. 2026-03-16T10:59:54Z 2019 Tuning of aggregation and film self-assembly of monomethincyanine dyes through variation of their monomer structure / M.M. Sieryk, O.P. Dimitriev // Semiconductor Physics Quantum Electronics & Optoelectronics. — 2019. — Т. 22, № 1. — С. 53-59. — Бібліогр.: 16 назв. — англ. 1560-8034 PACS: 78.40.Me, 81.16.Dn https://nasplib.isofts.kiev.ua/handle/123456789/215427 https://doi.org/10.15407/spqeo22.01.53 Formation of condensed films and solution aggregates of four different monomethincyanine dyes has been studied using optical absorption spectroscopy and simulation methods, depending on variation of the dye monomer structure. The structure of the molecular dimer as a basic unit for the formation of the condensed state was found to be largely dependent on heteroatoms in the dye structure and the presence of end hydrocarbon groups. The above factors mainly determine the mutual position of molecules in the dimer. It has been found that mutual orientation, intermolecular distance, and overlap of the adjacent molecules are the major factors influencing absorption spectra of dye aggregates. The dimer geometry that plays the primary role in film nucleation, however, has been shown to undergo changes depending on the temperature conditions or film thickness. We thank Dr. Yu. Slominskii for dyes granting, Dr. P. Lytvyn for the AFM studies, and Dr. K. Grytsenko for useful comments. en Інститут фізики напівпровідників імені В.Є. Лашкарьова НАН України Semiconductor Physics Quantum Electronics & Optoelectronics Hetero- and Low-Dimensional Structures Tuning of aggregation and film self-assembly of monomethincyanine dyes through variation of their monomer structure Article published earlier |
| spellingShingle | Tuning of aggregation and film self-assembly of monomethincyanine dyes through variation of their monomer structure Sieryk, M.M. Dimitriev, O.P. Hetero- and Low-Dimensional Structures |
| title | Tuning of aggregation and film self-assembly of monomethincyanine dyes through variation of their monomer structure |
| title_full | Tuning of aggregation and film self-assembly of monomethincyanine dyes through variation of their monomer structure |
| title_fullStr | Tuning of aggregation and film self-assembly of monomethincyanine dyes through variation of their monomer structure |
| title_full_unstemmed | Tuning of aggregation and film self-assembly of monomethincyanine dyes through variation of their monomer structure |
| title_short | Tuning of aggregation and film self-assembly of monomethincyanine dyes through variation of their monomer structure |
| title_sort | tuning of aggregation and film self-assembly of monomethincyanine dyes through variation of their monomer structure |
| topic | Hetero- and Low-Dimensional Structures |
| topic_facet | Hetero- and Low-Dimensional Structures |
| url | https://nasplib.isofts.kiev.ua/handle/123456789/215427 |
| work_keys_str_mv | AT sierykmm tuningofaggregationandfilmselfassemblyofmonomethincyaninedyesthroughvariationoftheirmonomerstructure AT dimitrievop tuningofaggregationandfilmselfassemblyofmonomethincyaninedyesthroughvariationoftheirmonomerstructure |