Single molecules of terrylene in di-substituted naphthalenes crystallizing in the herringbone pattern

Article abstract of DOI:10.1039/c6ra27167g

2,3-Dichloronaphthalene (2,3-DCN) and 2,3-dibromonaphthalene (2,3-DBN) were synthesized, purified and used to grow single crystals in the form of thin plates. X-ray crystallographic studies, performed for the first time, showed that molecules in both isostructural crystals are arranged in the herringbone pattern. These crystals, lightly doped with terrylene (Tr), appeared to be very good systems for optical single-molecule studies. Fluorescence excitation spectra of single Tr molecules at 5 K in excess of the dominating purely electronic (0, 0) and intense vibronic line of ～250 cm^-1 frequency had a new, “184 cm^-1” line, absent in the spectrum of isolated (D_2h) Tr. Quantum-chemistry calculations indicated that this new line was the fingerprint of the deformation of the Tr molecule in the crystal structure, which lowered its symmetry to C_2h

Full text of DOI:10.1039/c6ra27167g

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Single molecules of terrylene in di-substituted
naphthalenes crystallizing in the herringbone
pattern†
Cite this: RSC Adv., 2017, 7, 2780
Magda Białkowska,a Wojciech Chaładaj,b Irena Deperasinska,a
´
Aleksandra Drzewiecka-Antonik,a Anna E. Koziol,c Artur Makarewicza
a
*
and Bolesław Kozankiewicz
2,3-Dichloronaphthalene (2,3-DCN) and 2,3-dibromonaphthalene (2,3-DBN) were synthesized, purified
and used to grow single crystals in the form of thin plates. X-ray crystallographic studies, performed for
the first time, showed that molecules in both isostructural crystals are arranged in the herringbone
pattern. These crystals, lightly doped with terrylene (Tr), appeared to be very good systems for optical
single-molecule studies. Fluorescence excitation spectra of single Tr molecules at 5 K in excess of the
dominating purely electronic (0, 0) and intense vibronic line of ꢀ250 cmꢁ1 frequency had a new, “184
cmꢁ1” line, absent in the spectrum of isolated (D2h) Tr. Quantum-chemistry calculations indicated that
this new line was the fingerprint of the deformation of the Tr molecule in the crystal structure, which
Received 22nd November 2016
Accepted 13th December 2016
DOI: 10.1039/c6ra27167g
www.rsc.org/advances
lowered its symmetry to C2h.
to photo-oxidation. From this point of view convenient choice
are solid media, like molecular crystals where dopants occupy
well dened incorporation sites and experiments can be per-
formed in a broad temperature range, like in a case of terrylene
(Tr) in a p-terphenyl (p-T) crystal.6,7
Introduction
Optical detection of single molecules, more than 25 years aer
the rst reports,1,2 found multiple applications in a wide range
of elds like material science, quantum optics and biophysics.3,4
The main advantage of the single-molecule research is that it
removes ensemble-averaging and opens the door to study the
properties of the nano-world. Experiments are however difficult
and only a few molecule/matrix systems can be used for such an
optical study.
First of all a molecule for single-molecule optical research
has to be a very efficient emitter of uorescence photons. This
means a high absorption cross section for population of the
lowest excited singlet S1 state and high uorescence quantum
yield for the back, S1 / S0 transition with negligible inter-
system crossing to the long-lived triplet T1 state.5 Another
important requirement is that the molecule has to avoid photo-
bleaching (irreversible photo-reaction), at least for the time
sufficient to distinguish the uorescence photons from the
background signal of a detector. As a rule molecules are more
stable in rigid environments, especially if the bleaching is due
In order to improve the signal-to-background ratio the illu-
minated volume of a sample has to be as small as possible. In
addition to the use of a microscope objective, which focuses the
light to the diffraction limited spot, this requirement prefers the
use of a host crystal which can be obtained in a form of thin
plate. It is a case of linear aromatic polyacenes which crystallize
in the ‘herringbone’ pattern. It is also a case of 2,3-dime-
thylnaphthalene (2,3-DMN) crystal, which we already used as
a solid matrix to study single molecules of Tr.8 2,3-DMN crys-
tallizes in a perfectly ordered lattice, similar to that of anthra-
cene, but with ‘dipolar’ disorder of the constituting molecules.9
This disorder is manifested by broad (fwhm z 120 cmꢁ1 at 5 K)
inhomogeneous (0, 0) line in the uorescence excitation spec-
trum of an ensemble of Tr molecules.10 The success of using 2,3-
DMN as a transparent solid matrix for the single-molecule
studies encouraged us to extend investigations on single crys-
tals of 2,3-dichloronaphthalene (2,3-DCN) and 2,3-dibromo-
naphthalene (2,3-DBN). We expected that these compounds will
also crystallize in the herringbone pattern.
a
´
Institute of Physics, Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668 Warsaw,
Poland. E-mail: kozank@ifpan.edu.pl
bInstitute of Organic Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224
In the present work 2,3-DCN and 2,3-DBN were synthesized,
extensively puried and used to grow by sublimation the good
quality single crystals in the form of thin plates. To our surprise
the structures of 2,3-DCN and 2,3-DBN crystals were not known
(or at least not published) and therefore the X-ray crystallog-
raphy was used for their determination. Next, we grew single
Warsaw, Poland
cFaculty of Chemistry, Maria Curie-Skłodowska University, 20-031 Lublin, Poland
† Electronic supplementary information (ESI) available: Details of synthesis, NMR
spectra, additional optical results and details of quantum-chemistry calculations.
CCDC 1509875 and 1509878. For ESI and crystallographic data in CIF or other
electronic format see DOI: 10.1039/c6ra27167g
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Table 1 Crystal data and experimental parameters
crystals of 2,3-DCN and 2,3-DBN lightly doped with Tr by using
the technique of co-sublimation of both components. These
crystals were used for single-molecule optical studies, by
a confocal uorescence microscopy technique at 5 K with a low-
resolution laser excitation. The preliminary results of the
research were already published.11
In the work we concentrated on deformations of the molec-
ular structure of the guest, Tr, which were induced by the host
matrix. This information could be deduced from the structure
of uorescence excitation spectrum recorded at low tempera-
ture. Appearance of the new vibronic components, which were
absent in the planar form of Tr (D2h symmetry) indicated
deformations lowering the molecular symmetry. Analysis of the
spectra was performed with the aid of quantum-chemistry
calculations.
Compound
Formula
2,3-DCN
10H6Cl2
2,3-DBN
C10H6Br2
285.97
Orthorhombic
Pbca
11.692(3)
7.545(3)
20.193(5)
1781.3(10)
8
2.133
1088
4.38–75.17
ꢁ14 # h # 13
ꢁ9 # k # 9
ꢁ24 # l # 16
6251/1777/1357
C
Formula weight
Crystal system
Space group
197.05
Orthorhombic
Pbca
11.631(3)
7.417(2)
19.691(4)
1698.7(7)
8
˚
a [A]
˚
b [A]
˚
c [A]
3
˚
V [A ]
Z
d [g cmꢁ3
F(000)
]
1.541
800
q range for data collection [ꢂ]
4.49–74.04
ꢁ14 # h # 14
ꢁ6 # k # 8
ꢁ22 # l # 24
3238/1589/1160
Index ranges
Reections collected/
unique/observed [I > 2s(I)]
Goodness of t on F2
R1[I > 2s(I)]
Results and discussion
Synthesis of 2,3-DCN and 2,3-DBN
1.089
0.0788
1.004
0.0475
0.12
wR2[I > 2s(I)]
0.2002
Residual electron density
0.48; ꢁ0.71
0.98; ꢁ1.44
2,3-DCN was obtained from o-phthalaldehyde in three steps
according to Scheme 1. More details about the synthesis and the
intermediate products are given in the ESI.† Similar three step
strategy was utilized to synthesize 2,3-DBN. The nal products
(2,3-DCN and 2,3-DBN) were obtained in the form of white
crystals.
ꢁ3
˚
(max; min) [e A
]
X-ray structure analysis of 2,3-DCN and 2,3-DBN single
crystals
Single crystals of 2,3-DCN and 2,3-DBN were grown, from zone-
rened material, by sublimation under ꢀ0.2 bar of argon gas
atmosphere. The crystals, obtained in the form of thin plates,
were investigated by using the X-ray diffraction technique. The
crystallographic data, details of data collection and renement
are collected in Table 1.
Molecules of both compounds, 2,3-DCN and 2,3-DBN,
appeared to be planar in the crystal structure. The bond lengths
and valence angles of the aromatic rings are within the expected
ranges and their geometries are analogous to those found in
literature.12 The C–Cl and C–Br bond lengths of 2,3-DCN and
2,3-DBN molecules are similar to those observed in their
isomers.13
Molecules in the isostructural crystals are held together by
weak C–H/p, C–H/halogen and halogen/halogen intermo-
lecular interactions (e.g. Fig. 1 and S2 and Table S1 of the ESI†).
The C–H/Cl/Br contacts generate chains of molecules along
the c-axis. These head-to-tail chains are linked by Cl/Cl/Br/Br
interactions to form a sheet in the ac plane (Fig. 1a). Each of the
molecules within the sheet contacts with four neighbor
Fig. 1 (a) Sheet of 2,3-DBN molecules formed by a combination of C–
H/Br and Br/Br interactions, and (b) the C–H/p contacts. Inter-
molecular interactions are drawn as green dashed lines. Distances are
given in Angstroms.
molecules via C–H/p bonds (Fig. 1b). All these weak and
directional forces play an important role in stabilizing the
supramolecular architecture and the herringbone packing of
the molecules is observed in both crystals, as shown in Fig. 2.
Scheme 1
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Fig. 3 Fluorescence excitation spectra of a typical single molecule of
Tr in a 2,3-DCN crystal at 5 K, recorded with the laser excitation
intensities given above each spectrum.
investigated molecule located at 12 250 cmꢁ1) and two vibronic
lines shied 184 and 247 cmꢁ1 to higher energy. In the spec-
trum recorded under high excitation intensity (720 kW cmꢁ2),
when the zero-phonon lines were close to saturation, we
observed growth of the broad phonon-side band.10,16 Distribu-
tions of the energetic position of the (0, 0) lines and of the
vibronic frequencies monitored for some other Tr molecules in
the investigated crystals can be found in the ESI.† The vibronic
line “184 cmꢁ1” has not been observed in previously reported
spectra of single Tr molecules embedded in p-T, naphthalene
and 2,3-DMN crystals.10,16
Relative intensities of the three uorescence excitation lines
behaved differently with the rise of the laser excitation power (I).
The uorescence intensities in the maximum of the lines, R(I),
were plotted in Fig. 4. Fits to the experimental points were done
Fig. 2 Crystal packing viewed down the c-axis: 2,3-DCN – top and
2,3-DBN – bottom. Cl atoms green; Br atoms dark red.
according to the well-known saturation formula:17 R(I) ¼ RN
ꢃ
The detailed data describing the crystal structures are available
elsewhere.14 Let us mention here, that the crystal lattices of both
compounds are ordered, without the statistical disorder of the
atomic positions like that observed in 2,3-DMN crystal.9
Up to our best knowledge (and to surprise) the present work
is the rst report of the structures of 2,3-DCN and 2,3-DBN
crystals. The only one previously reported crystal structure of the
2,3-dihalogen substituted naphthalene, viz. 2,3-diiodonaph-
thalene, was published by Novak.15 Structural studies of several
other isomers of dibromo- and dichloro-naphthalenes revealed
that they do not form the herringbone arrangement. These
compounds are: 1,4-dibromo-, 1,5-dibromo-, 1,8-dibromo-, 2,6-
dibromo-, 1,4-dichloro- and 2,6-dichloro-naphthalenes.13
(I/Is)/(1 + (I/Is)), where RN is the fully saturated detection rate
and Is – the saturation intensity. The fully saturated detection
rate RN for the excitation to both vibronic states were, within
the experimental error, approximately two times higher than
that for excitation to the purely electronic state. This is typical
observation for Tr molecules, as already reported for other
matrices.10,16 Such a behavior is possible if the triplet T1 state
population rate constant is considerably smaller than the
depopulation rate of this state.16 Then, under the purely elec-
tronic excitation populations of the electronic ground S0 and
lowest excited S1 states can only reach equal values (1/2 in each
state), whereas under excitation to vibronic component pop-
ulation can be completely transferred from the S0 to S1 state.
The saturation intensity Is is inversely proportional to the
absorption cross section of the considered transition. Analysis
of this value is however difficult because Is depends also on the
Optical studies of single molecules of Tr in 2,3-DCN and 2,3-
DBN crystals
Typical uorescence excitation spectra for a single Tr molecule relative widths of absorption and excitation lines. We should
in a 2,3-DCN crystal, which were obtained when we focused the remind here, that in the experiment we used a laser with the
laser light on a bright spot in the uorescence excitation image line-width ꢀ1 cmꢁ1, approximately 3 orders of magnitude
and scanned the excitation frequency within the tuning range of broader than the homogeneous width of the purely electronic
our laser (operating with Rh6G), for the three indicated excita- excitation line but similar to the widths of the vibronic lines.
tion intensities, were shown in Fig. 3. The spectra composed of Thus, we had to use much higher laser intensities than in
the purely electronic (0, 0) line (with the maximum for the a typical experiment with a single-mode laser.
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Fig. 5 Fluorescence intensity correlation function of a single Tr
molecule in 2,3-DCN crystal at 5 K, detected at different excitation
laser intensities. Fits were done to the mono-exponential
dependences.
rate constant k23 ¼ 800 ꢄ 70 sꢁ1, whereas the rate constant of
depopulation of this state kT ¼ 2500 ꢄ 200 sꢁ1. For ve other
single Tr molecules investigated in this crystal the estimated
rate constants k23 were between 700 and 1300 sꢁ1, and the rate
constants kT between 1800 and 3600 sꢁ1. For each Tr molecule
the kT value was always 2–3 times bigger than that for k23, in
agreement with the conclusion derived from the analysis of the
Fig. 4 Saturation curves for the single Tr molecule which spectra are
shown in Fig. 3. (a) Fluorescence intensity in the maximum of the
purely electronic (0, 0) line; (b) for the vibronic 184 cmꢁ1 line, and (c)
for the vibronic 247 cmꢁ1 line. The power density scale is given in % of
the maximum available power, which was ꢀ1450 kW cmꢁ2. The fitting uorescence intensity saturation dependence. Both rate
parameters are given in corners of each figure.
constants were subject of increase with the rise of temperature,
but within the whole available temperature range, from 5 to 300
K, we were able to detect single molecules of Tr.11 By the same,
In order to get independent information about the triplet external heavy-atom effect on the dopants, Tr molecules, con-
population and depopulation rate constants we measured nected with the chlorine atoms in the crystalline 2,3-DCN, was
second order uorescence intensity correlation function g(2)(s) weak and did not quenched efficiently their uorescence. We
for six single Tr molecules in a 2,3-DCN crystal at 5 K. A set of rationalized such a situation in terms of the energy diagram of
such functions for the same single Tr molecule obtained at the electronic states of Tr, which prevents efficient spin–orbit
several different exciting light intensities was shown in Fig. 5. coupling between the singlet S1 and the triplet T1 and T2 states
The characteristic feature, observed for other Tr molecules in responsible for the intersystem crossing pathway.11,20 The bright
this matrix as well, was pretty good t to a single exponential and photostable single molecules of Tr were already detected in
decay dependence. It might indicate either extremely weak polycrystalline 1,2-21 and 1,4-dichlorobenzenes,22 both host
population of the long-lived triplet state spin sublevel, and/or matrices with heavy-atoms of chlorine.
fast spin-lattice relaxation equalizing population of the spin
The (0, 0) uorescence line of a bulk sample of Tr in a 2,3-
sublevels already at 5 K.18 Using the procedure described in our DBN crystal was slightly shied to higher energy as compare
previous article,19 we estimated for the molecule contributing to with that in 2,3-DCN crystal. The (0, 0) line onset was at 17 300
the decays presented in Fig. 4 that the triplet state population cmꢁ1 and the line maximum at 17 260 cmꢁ1 (see Fig. S5 in the
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ESI†). Fluorescence decays of a bulk sample were well tted to
mono-exponential dependence with the average decay time of
about 3.6 ns, not much different from that for Tr in several
solids lacking heavy-atoms.23 Such a result suggested that the
presence of the bromide heavy-atoms in the crystal, which
might lead to an increase of the intersystem crossing yield, did
not disturb signicantly the total depopulation yield of the
singlet S1 state. We succeeded to detect several single molecules
of Tr in a 2,3-DBN crystal which had their purely electronic (0, 0)
lines located between 17 283 and 17 290 cmꢁ1. Experiments
appeared however more difficult than those with 2,3-DCN
crystal because of lower photostability of Tr molecules in 2,3-
DBN crystal. We were not lucky to nd any single Tr molecule
photo-stable enough to collect a set of uorescence excitation
spectra as well as a set of uorescence intensity autocorrelation
functions at sufficiently high excitation laser powers required
for convincing estimation of the triplet T1 state population rate
constant. From the analysis of the uorescence intensity
correlation function, collected with the low intensity of exciting
light, we were only able to estimate the population rate constant
Fig. 6 (left) Structure of Tr molecule with the coordinate axes used in
this work (X axis perpendicular to YZ plane). (right) Calculated fluo-
rescence excitation spectrum of Tr (D2h symmetry). S0 state was
optimized by DFT B3LYP/6-31G(d,p) method, S1 state optimized by TD
DFT B3LYP/6-31G(d,p) method. Details about the geometry, vibronic
frequencies and Franck–Condon factors were given in Tables S2–S4
of the ESI.† Calculated energy of the (0, 0) transition (with the
correction for the zero-point energy) was 16 547 cmꢁ1
.
kT. It was between 30 000 and 55 000 sꢁ1, an order of magnitude our calculations (see Table S4 of the ESI†) in the low frequency
bigger than for Tr molecules in a 2,3-DCN crystal. The other range, close to 184 cmꢁ1, there were three vibrations: 7b2g, 8b3u
and 9au, which frequencies in the S1 state were 174, 181 and 206
cmꢁ1, respectively. All of them were out-of-plane vibrations and
were inactive in the S0 / S1 transition for planar Tr. Franck–
Condon principle predicts that the vibronic line should appear
in the S0 / S1 spectrum if the projection of the geometry
change between the initial and nal states onto the normal
modes of the nal states follows displacement vectors of the
behavior observed for Tr molecules in 2,3-DBN crystal was
moreover the same as that in 2,3-DCN crystal, although the
vibronic frequencies were slightly bigger (see Fig. S4 in the
ESI†).
Quantum-chemistry calculations
Electronic states and spectra of Tr molecules were already vibration.30 A good example is ꢀ247 cmꢁ1 (ag) vibration in iso-
subject of several quantum-chemistry studies.24–29 In the present
work we complemented our previous DFT B3LYP/6-31g(d,p)
calculations performed for Tr in the ground S0 state with the
calculations for the excited S1 state performed by TD DFT
B3LYP/6-31g(d,p). Details of Tr geometry and vibrational
frequencies in both states for isolated Tr were given in the ESI
(Tables S2 and S3†).
lated Tr, in which the displacement vectors point along the long
axis of the molecule,27,29 and the transition between the elec-
tronic S0 and S1 states is connected with the shortening of the
bond lengths between the central and the external naphthalene
moieties25 (see the structures presented in Table S5 of the ESI†).
Such a practical application of the Franck–Condon rule was
used by us to model the vibronic spectra of Tr where the
The lowest energy purely electronic S0 / S1 transition is of symmetry of molecule was lowered in the controllable way. We
used the Y and Z coordinates of Tr atoms like those calculated
for planar D2h molecule, whereas the X (out-of-plane) coordi-
nates in the ground S0 state were deformed proportionally to the
displacement vectors of the 7b2g, 8b3u and 9au vibrations. In the
model, we assumed that deformation in the X direction of the
excited Tr was much smaller than in the ground S0 state. It has
been known25 (see Table S5 of the ESI†) that Tr molecule aer
excitation to the S1 state shortens length of its long axis and
decreases the molecular volume from 3122.6 bohr3 per mole to
2914.1 bohr3 per mole. Tr molecule in the excited state has
a little more space in the occupied cavity and thus may have
more planar structure.25,26,28 Therefore, for the deformed Tr
molecules in the S1 state we used coordinates almost identical
(up to the fourth decimal place) as those for planar (D2h) Tr.
With the new coordinates (see Table S6 of the ESI†) the
the Ag / B1u symmetry (in the convention that long axis is Z,
short Y and axis Z is perpendicular to the molecule plane). It is
strongly allowed and polarized along the long axis of Tr.
Calculated vibronic structure of uorescence excitation spec-
trum for isolated, planar Tr molecule (D2h symmetry) was pre-
sented in Fig. 6. Vibronic excitation spectrum composed of ag
vibrations and in the low energy range (up to 300 cmꢁ1 aboꢁve1
the (0, 0) line) there was only single line of the 247 cm
frequency. Such a spectrum, composed of (0, 0) and ꢀ250 cmꢁ1
vibronic lines, was observed by us for single molecules of Tr
dispersed in p-T16 and 2,3-DMN crystals.10 It was however not
a case of Tr molecules in 2,3-DCN crystal investigated in this
work, because in the uorescence excitation spectrum in excess
of the vibronic 247 cmꢁ1 line we observed an extra vibronic line
separated from the purely electronic (0, 0) origin by 184 cmꢁ1
.
From the point of view of the symmetry selection rules molecular symmetry was lowered to C2h, C2v and D2, respec-
tively. Projections of the deformed structures of Tr molecule on
the different molecular planes were shown on the le side of
Fig. 7. The characteristic feature of “7b2g” deformation was out-
appearance of the additional lines visualizes lowering of the
symmetry of the investigated molecule, for example due to
interaction with the surrounding host molecules. According to
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Fig. 7 Structures of Tr molecule deformed proportionally to the displacement vectors of the 7b2g, 8b3u and 9au vibrations (left 3 columns) and
the corresponding calculated excitation spectra. New lines (absent in planar Tr) were marked by *. For better visualization of the deformations in
the out-of-plane direction (along the axis X) they were 15 times magnified.
of-plane tilting of the long axis of Tr where the external naph- preserved in two other, “8b3u” and “9au” deformations. All the
thalene moieties moved in the opposite directions resembling calculated frequencies of the vibrations of Tr molecule
the shape of letter “S”. Linearity of the long axis of molecule was deformed these ways were positive and were collected in Table
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S7 of the ESI.† Basing only on the symmetry rules we might
expect appearance of the new lines corresponding to vibrations
4 and 7 for Tr deformed to C2h symmetry, vibrations 3, 5 and 8
for Tr in C2v symmetry, and vibrations 1 and 9 for Tr in D2
symmetry. However, taking into account the Franck–Condon
factors the number of vibronic lines of the sufficiently high
intensity was reduced. Calculated vibronic spectra of the
deformed Tr molecules were plotted at the right side of Fig. 7,
whereas the numerical data were collected in Table S8 of the
ESI.† In Fig. 7, the new lines which were absent for planar Tr
were marked by *. Each spectrum of the deformed Tr had
characteristic additional line (next to the ag 247 cmꢁ1 line) and
lesser intensity line, which was combination of the vibration ag
with the characteristic vibration.
The distinct deformations of the Tr geometry which were
manifested in appearance of the new, closely in frequency lying
vibronic lines tended us to investigate possible deformations in
the crystalline environment. Calculations were performed with
the aid of ONIOM procedure included in the Gaussian 09
package. We assumed that a guest Tr molecule replaced in the
crystal structure three host molecules. For calculation of Tr
structure we used the high level of ONIOM, for calculation of
host crystal structure the low level of ONIOM. We considered
different insertion sites and the lowest energy conguration was
presented in Fig. 8. The long Tr axis in this site is nearly parallel
to the axis a of the crystal (more precisely the angles between
both axes were 5.8 and 9 degree in 2,3-DCN and 2,3-DBN crys-
tals, respectively), whereas the short axis of Tr is nearly parallel
to the axis c of the crystal (more precisely, the angles between
both axes were 2 and 5 degree in 2,3-DCN and 2,3-DBN crystals,
respectively). Energies of the (0, 0) transitions and frequencies
of the “ag” and “b2g” vibrations calculated with the aid of
different methods were collected in Table S10 of the ESI.†
According to calculations Tr in 2,3-DCN and 2,3-DBN crystals
was not a planar molecule (calculated coordinates were given in
Table S9 of the ESI†), nor a symmetric one. Lack of the
symmetry was caused by the surrounding host molecules which
differently interact with different moieties of the guest mole-
cule. To characterize the deformation in Fig. 9 we plotted
calculated bending of the long axis of Tr along the out-of-plane
(X) direction. It is easy to see that the calculated deformation of
Tr structure resembled the one which was obtained following
the “7b2g” vibration – see Fig. 7. Therefore it was not surprising
Fig. 9 Calculated out-of-plane bending (along the axis X) of the long
axis (Z) of Tr in 2,3-DCN crystal. Points present out-of-plane shift of
the X coordinates of the central carbon atoms of Tr molecule (for
better visualization the scale in this direction was magnified by 200
times) calculated with different bases. The considered carbon atoms in
Tr structure were marked with red color.
Fig. 10 Calculated vibronic intensities in the spectrum of Tr molecule
in a 2,3-DCN crystal estimated as the square of the scalar products of
the vectors describing geometrical differences in the electronic
ground S0 and lowest excited S1 states (see Table S9†).
that in the calculated spectrum, presented in Fig. 10, next to the
dominating “ag” vibronic line we got the “177 cmꢁ1” line,
relative of the “b2g” vibration in planar Tr. In the calculated
spectrum there were observed also some other lines, but with
much lower intensity, indicating that the symmetry of the
deformed Tr is similar to C2h, but not perfectly.
Experimental
Synthesis of 2,3-DCN and 2,3-DBN
Details of the synthesis are given in the ESI.†
X-ray crystallography
The diffraction data for 2,3-DCN and 2,3-DBN crystals were
collected on a SuperNova diffractometer at 120 K using the
˚
CuKa radiation (l ¼ 1.54184 A). The data were corrected for
Lorentz and polarization effects. A multi-scan absorption
correction was applied. The structures were solved by direct
methods using the SHELXS-97 program and rened by the full-
Fig. 8 Tr molecule (red) in 2,3-DCN crystal (Cl atoms marked by green
color), where Tr was surrounded by 36 host molecules. Optimization
of the structure with the aid of ONIOM (B3LYP/STO-3G:PM3) method. matrix least-squares method on F2 using the SHELXL-97
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program.31 The non-hydrogen atoms were rened with aniso-
The crystals lightly doped with Tr provided the very good
tropic displacement parameters. The C-bonded H-atoms were crystalline matrices for single molecule studies in the broad
positioned geometrically and allowed to ride on the attached temperature range, from liquid helium to room temperature.
atom.
The presence of heavy-atoms (Cl and Br) in the host crystals had
only a little inuence on the photo-physical parameters of the
single Tr molecules. Triplet state population and depopulation
rate constants were obtained from the analysis of uorescence
intensity correlation function and saturation of the vibronic
lines observed in the uorescence excitation spectrum. Negli-
gible inuence of the external heavy-atom effect on the inter-
system crossing channel depopulating the uorescence
emitting singlet S1 state can be explained with the aid of the
energy diagram of the electronic states of Tr, where the singlet
S1 state is located far above the triplet T1 state and below the T2
state. Thus, single molecules of Tr in the investigated crystals
are nearly as good emitters of uorescence photons as in the
systems without heavy-atoms.
Optical studies
Single crystals of zone-rened 2,3-DCN and 2,3-DBN lightly
doped with Tr (dopant concentration of the order of 10ꢁ12
moles per mole) were obtained by co-sublimation of both
components in argon gas atmosphere (ꢀ0.2 atm) at a tube
ꢂ
temperature close to 150 C. Tr was purchased from the Insti-
¨
tute fur PAH-Forschung (Greifenberg, Germany) and used as
received. Single crystals in the form of thin plates, especially
those of 2,3-DBN, appeared to be very fragile and had to be
treated with a big care in order to avoid breaking. Crystals were
attached to a sample holder and inserted into a cryostat, which
temperature could be stabilized at any value between 5 and 300
K. Cryostat was part of a home-made confocal microscope. The
excitation source was a Coherent 700 dye laser (operating with
Rh6G dye) pumped by a Verdi 5 laser: whole frequency 17 150–
17 600 cmꢁ1, spectral resolution ꢀ1 cmꢁ1. Laser light, applied
along the crystal axis c, was focused to a near-diffraction limited
spot of ꢀ0.45 mm diameter using a low temperature microscope
objective (Bernhard Halle Nach. GmbH, Berlin, Germany).
Fluorescence photons, transmitted through appropriate
dielectric lters, were detected with a SPCM-AQR 14 photon
counting module. More details about our confocal microscope
can be found elsewhere.10
Fluorescence excitation spectrum of single Tr molecules,
within the scanning range of our laser, composed of the
dominating purely electronic (0, 0) line, intense ag vibronic line
of ꢀ250 cmꢁ1 frequency and a new “184 cmꢁ1” line. This last
vibronic component is absent in the spectrum of isolated (D2h
)
Tr and was not observed in all previously investigated systems.
Appearance of the additional line in the uorescence exci-
tation spectrum visualizes deformation of the Tr molecule
structure due to the interactions with the surrounding crystal
molecules. Quantum-chemistry calculations performed for the
different possible insertion sites, where Tr replaced three host
molecules, allowed us to nd the lowest energy conguration,
where the short axis of Tr molecule, Y, is approximately parallel
to the axis c of the crystal. Tr molecule in this site has the
structure deformed like that induced by the “7b2g” vibration in
planar Tr. In this mode symmetry of the molecule is lowered
from D2h (characterizing planar Tr) to C2h. Calculated frequency
of the “7b2g” line, 177 cmꢁ1, is not far from the experimentally
Quantum-chemistry calculations
All calculations were done with the aid of the methods included
in the Gaussian 09 package.32 The molecular geometry of Tr was
conducted with B3LYP and TD B3LYP/6-31G(d,p) methods,
while the vibronic spectra with method described in ref. 33. Tr
in the crystals was treated by ONIOM methods, where Tr
(ONIOM high level) was described by B3LYP/6-31G(d,p) and
B3LYP/STO-3G methods, whereas the surrounding crystal
(ONIOM low level) was described by UFF and PM3 methods.
Geometry of Tr molecule was optimized in the electronic
ground S0 and in the lowest excited S1 states. Vibrational
frequencies for Tr in the crystal in the excited state were
calculated only with TD B3LYP/STO-3G method, due to a too
extended calculation time and a computer memory consump-
tion. Crystallographic parameters (coordinates of the atoms in
the molecule, and arrangement of molecules in the crystal unit)
were taken as obtained by the X-ray diffraction studies per-
formed in the present work.
determined 184 cmꢁ1
.
The theoretical approach presented in this work may be
applied to other systems where the surrounding matrix lowers
symmetry of the guest molecules.
Acknowledgements
The work was nancially supported by the National Science
Centre, Poland, grant no. 2015/17/B/ST2/01744. Theoretical
calculations were performed at the Interdisciplinary Centre of
Mathematical and Computer Modelling (ICM) of the Warsaw
University under computational grant no. G-32-10. X-ray crys-
tallographic studies were carried out with the aid of equipment
purchased thanks to the nancial support of the European
Regional Development Fund in the framework of the Opera-
tional Program Development of Eastern Poland 2007–2013
Conclusions
2,3-DCN and 2,3-DBN were synthesized and used to grow single (Contract No. POPW.01.03.00-06-009/11-00, Equipping the
crystals in the form of thin plates. The X-ray diffraction analysis laboratories of the Faculties of Biology and Biotechnology,
showed that the crystal structures of both compounds are Mathematics, Physics and Informatics, and Chemistry for
ordered where the weak and directional forces generate the studies of biologically active substances and environmental
herringbone packing of the constituting molecules.
samples).
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