Herringbone structures of 2,7-dihalogenated acridine tailored by halogen-halogen interactions

Article abstract of DOI:10.1016/j.molstruc.2015.03.042

The crystal structures of the 2,7-dibromo- and 2,7-diiodoacridines (2 and 3) were determined by single-crystal X-ray diffraction analysis. Molecules of the brominated 2 were assembled through different types of halogen-halogen interactions (Type-I and Type-II). Conversely, molecules of the iodinated 3 were assembled only through Type-II interactions. Although both compounds were packed in a herringbone way, the intermolecular π-π stacking was observed only in the brominated 2. In the solution and solid-state absorption spectra, a bathochromic shift in the absorption was observed, as the mass of the halogen atoms increased. Theoretical calculation indicated a substituent effect of the halogen on the π-orbital of the acridine moiety. In the solid state, the iodinated 3 exhibited a significant absorption in the orange-to-red wavelength region.

Full text of DOI:10.1016/j.molstruc.2015.03.042

Journal of Molecular Structure 1093 (2015) 59–64
Contents lists available at ScienceDirect
Journal of Molecular Structure
journal homepage: www.elsevier.com/locate/molstruc
Herringbone structures of 2,7-dihalogenated acridine
tailored by halogen–halogen interactions
⇑
Masaki Yamamura, Seira Ikuma, Tatsuya Nabeshima
Graduate School of Pure and Applied Sciences, Tsukuba Research Center for Interdisciplinary Materials Science (TIMS), University of Tsukuba, Tennodai 1-1-1, Tsukuba, Ibaraki
305-8571, Japan
h i g h l i g h t s
g r a p h i c a l a b s t r a c t
ꢀ
ꢀ
ꢀ
ꢀ
2,7-Dibromo- and 2,7-diiodoacridines
(2 and 3) were synthesized.
In the crystals, 2 and 3 were packed in
a herringbone way.
The Type-I and Type-II halogen–
halogen interactions were shown in 2.
Only the Type-II interaction was
shown in 3.
a r t i c l e i n f o
a b s t r a c t
Article history:
The crystal structures of the 2,7-dibromo- and 2,7-diiodoacridines (2 and 3) were determined by single-
crystal X-ray diffraction analysis. Molecules of the brominated 2 were assembled through different types
of halogen–halogen interactions (Type-I and Type-II). Conversely, molecules of the iodinated 3 were
assembled only through Type-II interactions. Although both compounds were packed in a herringbone
Received 19 January 2015
Received in revised form 20 March 2015
Accepted 23 March 2015
Available online 31 March 2015
way, the intermolecular
p–p stacking was observed only in the brominated 2. In the solution and
solid-state absorption spectra, a bathochromic shift in the absorption was observed, as the mass of the
halogen atoms increased. Theoretical calculation indicated a substituent effect of the halogen on the
Keywords:
Acridine
Herringbone
p–p stacking
Halogen–halogen interaction
p-orbital of the acridine moiety. In the solid state, the iodinated 3 exhibited a significant absorption in
the orange-to-red wavelength region.
Ó 2015 Elsevier B.V. All rights reserved.
Atoms-in-molecule
Introduction
crystallography, acridine is well known to crystallize in seven poly-
morphic forms [8–14]. The complicated polymorphism of acridine
The assembly of
p-conjugated compounds is of significant
is due to various intermolecular interactions, i.e., p–p, CH–p, and
interest because the physical and electronic properties signifi-
cantly depend on the intermolecular orientation of the compounds.
CH–N interactions. If the morphology of the acridine crystal can
be controlled, acridine could find application as an organic func-
tional material. The crystallization of acridine has been controlled
by utilizing solvents [15] or through the deuterium isotope effect
[16]. Halogen–halogen interactions are attractive forces that have
been utilized in crystal engineering [17–24]. Although halogen–
halogen interactions are a result of relatively weak van der
Waals forces, they can play a significant role in defining the ori-
entation of molecules [25]. Halogen–halogen interactions belong
Crystal engineering of
p-conjugated compounds is especially
important in the design of organic electronic materials such as
OFET [1] or OLED [2]. Acridine is often used as a luminophore
[3,4], electron–acceptor [5], and DNA-intercalator [6,7]. In
⇑
Corresponding author.
http://dx.doi.org/10.1016/j.molstruc.2015.03.042
0022-2860/Ó 2015 Elsevier B.V. All rights reserved.

60
M. Yamamura et al. / Journal of Molecular Structure 1093 (2015) 59–64
(a)
(b)
(c)
Scheme 1. HalogenÁ Á Áhalogen interactions. (a) Type-I interactions, (b) Type-II
interactions, and (c) polar flattening effect in halogenated organic compounds.
to two types based on their different geometries (Scheme 1)
[26–28]. Type-I is the van der Waals type interaction to afford a
symmetrical arrangement. Type-II is recognized as a Coulombic
donor–acceptor interaction to afford a perpendicular arrangement.
Allen concluded that halogens interact with nucleophiles in a
‘‘head-on’’ way and electrophiles in a ‘‘side-on’’ way (Scheme 1c)
[29]. The donor–acceptor interaction between halogens in the
Type-II way leads to an accurate molecular arrangement. The
Type-II interaction is dominant when going from Cl to I because
the heavier atom becomes more polarized.
Fig. 1. ORTEP drawing of 2 with the 50% probability ellipsoid from (a) top and (b)
side views.
Despite the importance of both acridine and halogen–halogen
interactions, there have been only two reports of crystallographic
analysis of halogenated acridines without any other substituents;
9-chloroacridine [30] and 3,5,6,7,8-pentafluoroacridine [31].
Halogen–halogen interaction was seen only in 3,5,6,7,8-pentafluo-
roacridine. However, there are no reports of the structural analysis
of acridines bearing heavier halogen atoms, which afford stronger
interactions than fluorine. We have now synthesized and crystal-
lized acridine derivatives bearing bromine or iodine, which are
expected to form crystal structures that are controlled by halo-
gen–halogen interactions.
Results and discussions
2,7-Dibromoacridine (2) was synthesized from acridine (1)
according to the literature procedure [32] (Scheme 2). This
synthetic method selectively gives 2 without any other multi-
brominated products. 2,7-Diiodoacridine was synthesized by the
iodination of 2 with KI and CuI [33]. In this study, crystallographic
analysis of the compounds was initially performed.
Fig. 2. ORTEP drawing of 3 with the 50% probability ellipsoid from (a) top and (b)
side views.
Herringbone structures, which are generally observed in linear p-
Single-crystal X-ray diffraction analysis was used to determine
the crystal structures of 2 and 3. ORTEP diagrams are shown in
Figs. 1 and 2. One molecule of 2 is present in an asymmetric unit.
Compound 3 is positioned at the center of the mirror plane. The
geometries of 1–3 were optimized by DFT calculation at the
CAM-B3LYP/DGTZVP level. The structural parameters of both
experimental and calculated structures of 1–3 are shown in
Table 1. The theoretical calculation well reproduced the experi-
mental structures within the deviation of DFT calculation. The acri-
dine moieties are nearly planar with root-mean square deviations
(RMSD) of 0.022 and 0.037 Å for 2 and 3, respectively. The two bro-
mine atoms of 2, Br1 and Br2, are slightly separated from the least-
square plane with the distances of 0.064 and 0.186 Å, respectively.
The iodine atoms of 3 are also separated by a distance of 0.318 Å.
These values indicate a more planar structure for 2 than for 3.
conjugated molecules, are important for high performance organic
materials [34,35]. Noteworthy is that the bromine atoms make
contact with each other in the crystal of 2 (Fig. 3b). This fact sug-
gests that the assembly of the bromine atoms plays an important
role in the construction of the packing structure.
In the crystal of 3, molecules are arranged in a herringbone way
(Fig. 4a) with the non-centrosymmetric space group Cmc21. In con-
trast to 2, there is no p–p stacking in 3. The iodine atoms contact
each other in a similar way to 2 (Fig. 4b).
We investigated the closely located halogen atoms to shed light
on the halogen–halogen interaction (Table 2). In the crystal 2, one
bromine atom contacts with two other bromine atoms with dis-
tances of 3.668 and 3.708(3) Å. These values are close to the sum
of the van der Waals radii, 3.70 Å, suggesting halogen–halogen
interactions. In the Br1Á Á ÁBr2i contact, the carbon–halogen–
halogen angles, h1 and h2, are 141.0° and 127.6°, respectively. The
h1 and h2 values indicate a Type-I interaction. On the other hand,
In the crystal of 2, a
action with a distance of 3.3660(6) Å (Fig. 3a). The
arranged in herringbone way with space group P21/c.
p
dimer is formed through a stacking inter-
p
dimers are
a
Scheme 2. Synthesis of 2,7-halogenated acridines.

M. Yamamura et al. / Journal of Molecular Structure 1093 (2015) 59–64
61
Table 1
Selected bond lengths (Å), bond angles (°) torsion angles (°), and RMSDs in the
acridine units (Å) of experimental and calculated structures of 1–3.
Experimental
Calculated
1
C1–N1 (Å)
C2–N1 (Å)
C1–N1–C2 (°)
RMSD (Å)
1.347
1.348
117.7
0.034
1.339
1.339
118.5
0
2
C4–N1 (Å)
C5–N1 (Å)
Br1–C1 (Å)
Br2–C8 (Å)
C4–N1–C5 (°)
RMSD (Å)
1.347(3)
1.349(3)
1.898(2)
1.898(2)
117.5(2)
0.022
1.338
1.338
1.902
1.902
118.4
0
3
C2–N1 (Å)
I1–C4 (Å)
1.344(7)
2.086(4)
117.9(9)
0.037
1.338
2.110
118.4
0
C2–N1–C2i (°)
RMSD (Å)
Symmetric operation, i: –x, +y, +z.
the Br1Á Á ÁBr2ii contact exhibited very different h1 and h2 values of
166.6° and 113.4°, which indicate a Type-II interaction. Thus, the
packing of
2 is constructed through two different types of
halogen–halogen interactions. In crystal 3, one iodine atom also
contacts with two other iodine atoms with the crystallographically
identical distance of 4.063 Å, close to the IÁ Á ÁI van der Waals
distance 4.05 Å. The h1 value of the IÁ Á ÁIiii contact, 156.5°, is much
larger than the h2 value of 101.8°. Thus, the packing of 3 is
constructed though only Type-II interactions. The fact that the
intermolecular
p–p stacking was observed only in brominated 2
Fig. 3. Packing diagram of 2 from (a) a-axis and (b) c-axis.
might result from the difference in their halogen–halogen
interactions.
Theoretical calculations were performed to gain insight into the
halogen–halogen interactions. An atoms-in-molecule (AIM) analy-
sis [36] for the geometry of the contacted molecules of 3 gave the
charge density
q(r) and the Laplacian Dq(r) map (Fig. 5). A bond
critical point (BCP) is observed in the center of the two iodine
atoms. The existence of BCP is clearly indicative of the interatomic
interaction. In the BCP, the
general, a negative value of the Laplacian
q
(r) value is +6.5  10–3 e åÀ3. In
Dq(r) at the BPC indi-
cates that the atomic interaction is predominantly a closed-shell
interaction, while a positive value of (r) indicates that it is
dominated by shared electron (covalent) interactions. The (r)
D
q
D
q
values at the BPC between the iodine atoms is the negative value
of –4.0  10–3 e åÀ5, which is indicative of the closed-shell interac-
tion. These results are consistent with the reported AIM analysis
for the ClÁ Á ÁCl interaction [37].
Thermal gravimetric analysis of 2 and 3 showed sharp, two-step
mass losses (Fig. 6). Differential thermal analysis showed exother-
mic peaks when the mass loss started. These results suggested that
most of compounds was sublimated against the intermolecular
interactions. The onset temperatures were 210 and 276 °C for 2
and 3, respectively. These values are higher than that of 1, 179 °C
[38]. Thus, the halogen–halogen interactions appear to contribute
to the stabilization of the crystalline state, and the I–I interactions
in 3 are probably stronger than the Br–Br interactions in 2.
The UV–vis absorption spectra of 1–3 were measured in DMSO
(Fig. 7). All the compounds showed an absorption in the 300–
400 nm region. The absorption-maximum wavelength increases
(357 nm for 1, 368 nm for 2, 374 nm for 3) as the mass of the
bounded atoms, H (1), Br (2), or I (3), increases. A time-dependent
DFT calculation was performed to clarify the spectra (Fig. 8 and
Fig. 4. Packing diagram of 3 from (a) a-axis and (b) b-axis.
order of 1–3. The lowest singlet excitation states (S1) for 1–3 were
assigned to the
p
–
p
⁄ transitions of the acridine units. The excita-
tion energies for S1 decreased in the same order as the gaps.
Thus, the substituent effect on the spectra is due to the orbital
interaction of the acridine p-orbital with the halogen atoms.
In the reflectance spectra of the powdered samples of 1–3, a
red-shifted broad absorption was observed and compared to the
solution spectra. The absorbance above 600 nm is in the order of
1–3. The iodinated 3 exhibited a significant absorption in the
Table 3). The HOMOs and LUMOs are assigned to the
p orbitals
of the acridine moiety. The HOMO–LUMO gaps decrease in the

62
M. Yamamura et al. / Journal of Molecular Structure 1093 (2015) 59–64
Table 2
Halogen–halogen distances (d), carbon–halogen–halogen angles (h1 and h2), and
carbon–halogen–halogen–carbon torsion angles (/) in 2 and 3.
d (Å)
h1 (°)
h2 (°)
/ (°)
Br1Á Á ÁBr2i
Br1Á Á ÁBr2ii
I1Á Á ÁI1iii
3.668
3.708
4.063
141.0
166.6
156.5
127.6
113.4
101.8
106.5
147.5
155.9
Symmetric operation, i: –1 + x, 1/2–y, –1/2 + z, ii: –1 + x, +y, –1 + z, iii: 1/2–x, 1/2–y,
1/2 + z or –1/2 + x, 1/2–y, 1/2 + z.
orange-to-red region, 500–700 nm. The far-shifted absorption
might be ascribed to the intermolecular interactions of the
acridines.
The luminescence spectra of 1–3 are sharp, mirror images of the
absorption spectra (Fig. 9). The maximum wavelengths (409 nm
for 1, 424 nm for 2, 428 nm for 3) are in the order of those in the
absorption spectra.
Experimental
Materials and methods
All chemicals were reagent grade and used without further pur-
ification. All reactions were performed under nitrogen atmosphere.
The NMR spectra were recorded on Bruker AVANCE400 (400 MHz)
spectrometer. Deuterated solvents were purchased from
Cambridge Isotope Laboratories and used as received. In the NMR
measurements, tetramethylsilane was used as the internal standard
(0 ppm). UV–vis absorption spectra were recorded on JASCO Ubest
V-670. Solid-state reflectance spectra were measured by using an
integrating sphere instrument equipping with the spectrometer.
Gas chromatography–mass spectra were recorded on Shimazu
QP-2100 by electron-ionization method. Elemental analysis was
performed in Department of Chemistry, University of Tsukuba.
Synthesis of 2,7-dibromoacridine (2)
2,7-Dibromoacridine (2) was prepared according to the litera-
ture [32]. Pale yellow powder, yield 76%: 1H NMR (400 MHz,
Fig. 6. Thermal gravimetric and differential thermal analyses of (a) 2 and (b) 3.
DMSO-d6):
d 9.19 (s, 1H), 8.57 (d, J = 2.2 Hz, 2H), 8.14 (d,
J = 9.2 Hz, 2H), 8.04 (dd, J = 9.2, 2.2 Hz, 2H); MS (EI): m/z = 337
[M]+. Anal for C13H7NBr2, C; 46.33, H; 2.09, N; 4.16; found, C;
46.04, H; 2.04, N; 4.00.
Synthesis of 2,7-diiodoacridine (3)
A mixture of 2,7-dibromoacridine (2) (337 mg, 1.00 mmol), KI
(5.01 g, 30.2 mmol), and CuI (1.90 g, 9.97 mmol) in HMPA
(10 mL) was stirred at 155 °C for 72 h. After the reaction mixture
was cooled to room temperature, 100 mL of water was added.
Brown precipitate was collected and then Soxhlet extraction with
toluene gave pale brown solid. Crystallization of crude solid from
ethyl acetate gave yellow powder of 3 (101 mg, 23%). 1H NMR
(400 MHz, DMSO-d6): d 8.99 (s, 1H), 8.68 (d, J = 2.0 Hz, 2H), 8.08
(dd, J = 9.2, 2.0 Hz, 2H), 7.92 (d, J = 9.2 Hz, 2H); MS (EI): m/z = 443
[M]+. Anal for C13H7NI2, C; 36.23, H; 1.64, N; 3.25; found, C;
36.05, H; 1.65, N; 3.13.
Fig. 5. Calculated
Dq(r) maps in the C–IÁ Á ÁI–C plane. The positive and negative
X-ray crystallographic analysis
values are represented in green and black colors, respectively. Only an IÁ Á ÁI BCP is
depicted, while the other BCPs ascribed to intermolecular bonding are omitted. (For
interpretation of the references to colour in this figure legend, the reader is referred
to the web version of this article.)
Single crystals of 2 and 3 suitable for X-ray diffraction were
obtained by recrystallization from the hot-DMSO solution. The

M. Yamamura et al. / Journal of Molecular Structure 1093 (2015) 59–64
63
Fig. 7. UV–vis absorption spectra (lines) in DMSO (2.5 Â 10À5 M) and reflectance
spectra of powder samples (dots) of
1 (black), 2 (red), and 3 (blue). (For
Fig. 9. Luminescence spectra of 1 (black), 2 (red), and 3 (blue) in DMSO (2.5 Â 10À5
M, excited at 380 nm). (For interpretation of the references to colour in this figure
legend, the reader is referred to the web version of this article.)
interpretation of the references to colour in this figure legend, the reader is
referred to the web version of this article.)
Table 4
Crystallographic data of 2 and 3.
2
3
Formula
C
13H7NBr2
C13H7NI2
431.00
0.20 Â 0.10 Â 0.05
Orthorhombic
Cmc21
27.058(4)
7.0233(9)
6.0636(7)
90
Formula weight
Crystal size (mm3)
Crystal system
Space group
a (Å)
337.02
0.20 Â 0.20 Â 0.03
Monoclinic
P21/c
13.088(3)
14.226(3)
5.9330(12)
90
b (Å)
c (Å)
a
(°)
b (°)
97.624(2)
90
1094.9(4)
4
90
90
1152.3(2)
4
2.484
c
(°)
V (Å3)
Z
Dcalcd (g cm–3
)
2.045
Fig. 8. Kohn–Sham frontier orbitals of 1–3 at the CAM-B3LYP/DGTZVP level.
Collected/unique
Rint
6100/2457
0.0622
3075/1257
0.0185
hmax (°)
F000
27.571
648
7.370
–16 6 h 615
–18 6 k 618
–7 6 l 66
145/0
1.065
0.0342
27.545
792
5.427
–35 6 h 631
–9 6 k 65
–7 6 l 67
76/0
1.020
0.0135
Table 3
l
(Mo K
a
) (mm–1
)
Calculated singlet excited energies of 1–3 at the CAM-B3LYP/DGTZVP level.
Limiting indices
Transition (composition)
Excitation energy (nm)
(oscillator strength)
Parameters/restraints
1
2
3
S1
S1
S1
HOMO ? LUMO (97%)
HOMO ? LUMO (97%)
HOMO ? LUMO (96%)
333 (0.0742)
337 (0.0544)
340 (0.0462)
Goodness of fit (F2)
R1 (I > 2
wR2 (all date)
r
(I))
0.0938
0.0334
P
P
P
P
R1
=
||Fo|–|Fc|/ |Fo|, wR2 = { [w(F2o–Fc2)2]/ [w(Fo2)2]}1/2
.
X-ray diffraction intensities were collected on a CCD diffractometer
at 120 K using Mo K (graphite-monochromated, k = 0.71073 Å)
Thermal analyses
a
radiation. The data were integrated with SAINT (Bruker, 2007),
and an empirical absorption correction was applied with SADABS
(Bruker, 2007). The structure was solved by the direct method
of SHELXS-97 and refined using the SHELXL-97 program [39].
All of the positional parameters and thermal parameters of
non-hydrogen atoms were anisotropically refined on F2 by the
full-matrix least-squares method. Hydrogen atoms were placed
at the calculated positions (C–H = 0.95 Å) and refined riding on
their corresponding carbon atoms with Uiso(H) = 1.2Ueq(C).
Structural refinement of 3 was completed as a perfect racemic
twining (operation: –1000–1000–1). The crystallographic data
are listed in Table 4. The detailed crystallographic information files
(CIFs) have been deposited in the Cambridge Crystallographic
Database Centre (CCDC). Deposits numbered CCDC-1043816 and
1043817 contain the supplementary crystallographic data for
structures 2 and 3, respectively.
Thermal gravimetric and differential thermal analyses were
performed at the same time on Seiko Instruments Inc.
EXSTAR7000: TG/DTA7300 in the Chemical Analysis Center at the
University of Tsukuba. Samples were placed in aluminum pans
and heated at a constant rate of 5 °C/min under argon atmosphere.
Alumina powder was used as a reference.
a
Computational study
Quantum chemical calculations were performed using Gaussian
09 software [40]. The geometries for single molecules are opti-
mized using the CAM-B3LYP functional [41] with DGTZVP basis
set [42]. Time Dependent Density Functional Theory (TD-DFT)
was used for the vertical excitation energies and oscillator
strengths at the optimized geometries. Atoms-in-molecule (AIM)

64
M. Yamamura et al. / Journal of Molecular Structure 1093 (2015) 59–64
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Conclusion
The crystal structures of the 2,7-dibromo- and 2,7-diiodoacridi-
nes (2 and 3) were determined by single-crystal X-ray diffraction
analysis. Although both compounds were packed in a herringbone
way, the intermolecular
p–p stacking was observed only in the
brominated 2. Interestingly, alternative-layers of acridine and the
halogen were constructed in both crystals. The halogen–halogen
bonding was characterized by X-ray and AIM analyses. Molecules
of the brominated 2 were assembled through different types of
halogen–halogen interactions (Type-I and Type-II). Conversely,
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molecules of the iodinated
3 were assembled only through
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halogen interactions based on the contact angles: contacts with |h1–h2| 6 15°
are type I and contacts with 30° 6 |h1–h2| are type II. Contacts with 15° < |h1–
h2| < 30° are quasi-type I/type II. (See: A. Mukherjee, S. Tothadi, G.R. Desiraju,
Acc. Chem. Res. 47 (2014) 2514).
Type-II interactions. Thermal analysis supported that the
halogen–halogen interactions stabilize the crystal of acridine. In
the absorption and luminescence spectra, a bathochromic shift
was observed, as the mass of the halogen atoms increased.
Theoretical calculation indicated a substituent effect of the halogen
on the p-orbital of the acridine moiety. In the solid state, the iodi-
nated 3 exhibited a significant absorption in the orange-to-red
region. We will investigate the relationship between crystal struc-
tures and solid-state spectra. This study demonstrated that the
halogen–halogen interactions afford the herringbone assembly of
acridine, and the assembled structures are dependent on different
types of interactions.
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uk/conts/retrieving.html, or from the Cambridge Crystallographic
Data Centre, 12, Union Road, Cambridge CB2 1EZ, UK [Fax: +44
1223 336 033; e-mail: deposit@ccdc.cam.ac.uk]. Supplementary
data associated with this article can be found, in the online version,
at http://dx.doi.org/10.1016/j.molstruc.2015.03.042. These data
include MOL files and InChiKeys of the most important compounds
described in this article.
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