Supramolecular Synthesis Based on a Combination of Se?N Secondary Bonding Interactions with Hydrogen and Halogen Bonds

Article abstract of DOI:10.1021/acs.cgd.5b01356

Examination of the solid state structures of 2,1,3-benzoselenadiazole complexes with hydrogen or halogen bond donors has demonstrated that the 2,1,3-benzoselenadiazole molecules preferably form centrosymmetric dimers with use of [Se-N]₂ supramolecular synthon, whereas the two remaining nitrogen atoms not involved in the [Se-N]₂ supramolecular interactions can act as acceptors of hydrogen or halogen bonds. Cocrystallization of selenadiazoles with monofunctional hydrogen or halogen bond donors like pentafluorophenol, pentafluorobenzoic acid, or pentafluoroiodobenzene results in formation of binary discrete complexes. One- or two-dimensional aggregates based on selenadiazole [Se-N]₂ dimers as building blocks were prepared using bifunctional hydrogen or halogen bond donors like resorcinol, tetrafluororesorcinol, tetrafluorohydroquinone, and 1,4-diiodotetrafluorobenzene. During the complexation of selenadiazoles with hydroquinone, anilic acid, or chloranilic acid a competition between Se?N and Se?O interactions resulted in breaking of the [Se-N]₂ synthon.

Full text of DOI:10.1021/acs.cgd.5b01356

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Article
Supramolecular synthesis based on a combination of Se•••N
secondary bonding interactions with hydrogen and halogen bonds
Katarzyna Eichstaedt, Aleksandra Wasilewska, Barbara Wicher, Maria Gdaniec, and Tadeusz Po#o#ski
Cryst. Growth Des., Just Accepted Manuscript • DOI: 10.1021/acs.cgd.5b01356 • Publication Date (Web): 13 Jan 2016
Downloaded from http://pubs.acs.org on January 25, 2016
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Supramolecular synthesis based on a combination of Se···N secondary bonding
interactions with hydrogen and halogen bonds
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Katarzyna Eichstaedt,† Aleksandra Wasilewska,† Barbara Wicher ‡ Maria Gdaniec*§ and
Tadeusz Połoński*†
†Department of Chemistry, Technical University, 80-233 Gdańsk, Poland, §Faculty of
Chemistry, A. Mickiewicz University, 61-614 Poznań, Poland, ‡Department of Chemical
Technology of Drugs, Poznan University of Medical Sciences, 60-780 Poznań, Poland
The crystal structures of cocrystals of 2,1,3-benzoselenadiazoles with hydrogen or halogen bond
donors have demonstrated that the [Se–N]2 cyclic supramolecular synthon based on Se···N
secondary bonding interaction (SBI) is quite reliable. The [Se–N]2 dimers were found in 9 out of
the 12 studied cocrystals and in two polymorphic forms of 4,5,6,7-tetramethyl-2,1,3-
benzoselenadiazole. These studies show that the [Se–N]2 dimer can be used as a secondary
building block for the construction of larger supramolecular assemblies or frameworks. It can
bind to the molecules containing hydrogen- or halogen-bond donors and in some cases form
additional SBIs with the use of selenadiazole binding sites that are not involved in the formation
of the dimers. Binary discrete complexes were formed with monofunctional hydrogen or halogen
bond donors like pentafluorophenol, pentafluorobenzoic acid or pentafluoroiodobenzene whereas
one or two dimensional aggregates were found in complexes with bifunctional donors like
resorcinol, tetrafluororesorcinol, tetrafluorohydroquinone and 1,4-diiodotetrafluorobenzene. It
has been demonstrated that carboxylic acids and ortho-fluorophenols bind to the [Se–N]2 dimers
via cyclic synthons based on a combination of the O–H···N and N–Se···X (X = F, O)
interactions. In turn, the geometry of the C–I···N halogen bond does not allow for the formation
of an analogous cyclic synthon in the cocrystals of selenadiazoles with ortho-
flouroiodobenzenes.
e-mail: magdan@amu.edu.pl; Tel: +48 61 8291684 ; e-mail: tadpolon@pg.gda.pl; Tel: +48 +48 58 3471528
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Supramolecular synthesis based on a combination of
Se···N secondary bonding interactions with
hydrogen and halogen bonds
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Katarzyna Eichstaedt,† Aleksandra Wasilewska,† Barbara Wicher ‡ Maria Gdaniec*§ and
Tadeusz Połoński*†
†Department of Chemistry, Technical University, 80-233 Gdańsk, Poland, §Faculty of
Chemistry, A. Mickiewicz University, 61-614 Poznań, Poland, ‡Department of Chemical
Technology of Drugs, Poznan University of Medical Sciences, 60-780 Poznań, Poland
KEYWORDS: crystal engineering, secondary bonding interactions, cocrystals, 2,1,3-
benzoselenadiazoles, crystal structure
RECEIVED DATE
ABSTRACT: Examination of the solid state structures of 2,1,3-benzoselenadiazole complexes
with hydrogen or halogen bond donors has demonstrated that the 2,1,3-benzoselenadiazole
molecules preferably form centrosymmetric dimers with use of [Se–N]2 supramolecular synthon
whereas the two remaining nitrogen atoms not involved in the [Se–N]2 supramolecular
interactions can act as acceptors of hydrogen or halogen bonds. Cocrystallization of
selenadiazoles with monofunctional hydrogen or halogen bond donors like pentafluorophenol,
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pentafluorobenzoic acid or pentafluoroiodobenzene results in formation of binary discrete
complexes. One or two dimensional aggregates based on selenadiazole [Se–N]2 dimers as
building blocks were prepared using bifunctional hydrogen or halogen bond donors like
resorcinol, tetrafluororesorcinol, tetrafluorohydroquinone and 1,4-diiodotetrafluorobenzene.
During the complexation of selenadiazoles with hydroquinone, anilic acid or chloranilic acid a
competition between Se···N and Se···O interactions resulted in breaking of the [Se–N]2 synthon.
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Introduction
Secondary bonding interactions (SBIs) are of primary importance for supramolecular
chemistry.1-2 There is a close analogy between X–A⋅⋅⋅Y SBIs and hydrogen bonding: both
systems are basically linear, where X–A is a covalent bond and A⋅⋅⋅Y is a weak interaction.
When A = H this interaction is described as a hydrogen bond and for A
H as a secondary
bond. In specific cases when A is halogen, chalcogen or pnictogen atom these secondary
interactions are also called halogen, chalcogen or pnictogen bonds, respectively.3-9 The X–A⋅⋅⋅Y
interaction is strengthened by the presence of an electronegative substituent on the electron-
acceptor atom A and it gains strength as one moves down to heavier elements in the appropriate
column of the periodic table. According to so called σ-hole theory,10-12 noncovalent X-A⋅⋅⋅Y
interaction between covalently-bonded atom A of Group IV-VII and a negative site Y involves a
region of positive electrostatic potential, labeled a σ-hole, on the extension of the covalent bonds
to the Group IV – VII atom. The features and properties of halogen, chalcogen or pnictogen
bonds treated as σ-hole bonds are explained in terms of electrostatics, polarization and
dispersion.
Scheme 1
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1,2,5-Chalcogenadiazoles exhibit a remarkable tendency toward self-association into dimers
and polymers by four-membered [Se–N]2 or [Te–N]2 cyclic supramolecular synthons (Scheme 1)
involving two highly directional SBIs.13-20 The strength of SBIs formed by 1,2,5-
chalcogenadiazoles increases on going from sulphur to tellurium and as revealed by a survey of
the Cambridge Structural Database (CSD)21 telluradiazoles frequently form polymers by [Te–N]2
synthons, selenadiazoles form dimers whereas thiadiazoles22 most often are not associated.
We turned our attention to 2,1,3-benzoselenadiazoles which have attracted much less attention
than analogous telluradiazoles showing stronger SBIs. These compounds are easily accessible in
reaction of o-phenylenediamines with selenium dioxide24 and are much better soluble in common
organic solvents than the tellurium derivatives. Structural studies of several compounds of this
class have demonstrated that due to self-complementary Se···N interactions they crystallize in a
dimeric form (Fig. 1a-b).22,25-27 Interestingly, the parent 2,1,3-benzoselenadiazole (1) shows
different behavior and the SBIs lead to a catemer motif in the solid state (Fig. 1c).28
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Figure. 1 a) Electrostatic potential map for 1 showing two σ-holes at the extension of N-Se
bonds; b) dimeric and c) catemeric motifs via Se···N secondary interactions.
However, the dimeric units of 1 have been found in its cationic form as well as in some metal
complexes of this compound.29-35 The 2,1,3-benzoselenadiazole dimers that are potential
ditopic ligands for metal coordination have been recently used for the preparation of
coordination polymers.32-35 Thus, it seems reasonable to expect that such dimers could be also
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used as building blocks for the construction of extended supramolecular frameworks with use of
two remaining sp2 nitrogen atoms not involved in the formation of a [Se–N]2 synthon.
These N atoms create two potential acceptor sites for hydrogen, halogen or chalcogen bonds.
This however raises the problem of competition of intermolecular interactions that might result
in a disruption of the dimer structure and poses difficulties in the design and construction of
ordered supramolecular architectures with use of the title compounds. More detailed studies of
the structural competition between Se···N interactions and hydrogen or halogen bonding could
help to develop supramolecular strategies that may accommodate two or more different
interactions in such a way that they could produce predictable supramolecular assemblies.
Last but not least, the polar 2,1,3-benzoselenadiazole molecules may be engaged in aromatic-
ring stacking interactions that, in general, should be orthogonal to the dimer plane. The self-
association of these heterocyclic molecules via aromatic interactions may compete with the
interactions involving aromatic rings bearing hydrogen or halogen bond donors. This
competition should be particularly important in the case of single hydrogen or halogen bond
donors attached to a perfluoroaryl skeleton as the aryl-perfluoroaryl interactions are particularly
strong.36-37
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In this contribution we report examples of supramolecular arrays created by complexation of
2,1,3-benzoselenadiazole (1) and its tetramethyl derivative (2) with several strong hydrogen
bond donors, which include: resorcinol (res), hydroquinone (hqu), anilic acid (ani), chloranilic
acid (cla), pentafluorophenol (pfp), pentafluorobenzoic acid (pfb), tetrafluororesorcinol (tfr) and
tetrafluorohydroquinone (tfq). For comparison we also prepared the complex of 2,1,3-
benzothiadiazole (3) with pfp. In the next step we studied structures of the complexes of 1 and 2
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with halogen bond donors including pentafluoroiodobenzene (pfi), 1,4-diiodotetrafluorobenzene
(dib), and iodine (I2) (see Scheme 2).
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Scheme 2. Chemical structures of the substrates
Experimental
2,1,3-Benzoselenadiazole (1) An aqueous solution of selenium dioxide (2.31 g, 21 mmol) was
added to 1,2-diaminobenzene (2.25 g, 21 mmol) in ethanol (15 mL), refluxed for 10’ and cooled.
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The collected white precipitate was recrystallized from hexane obtaining 3.85 g of the product;
m.p. 78–79 oC (lit.38,39 m.p. 76 oC).
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4,5,6,7-Tetramethyl -2,1,3-benzoselenadiazole (2) was obtained in a similar manner to 1;
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o
1
m.p. 159–160 C. H NMR (CDCl3) δ 2.68 (s, 6H), 2.68 (s, 2H), 2.35 (s, 6H); 13C NMR
(CDCl3) δ 160.3, 137.2, 125.7, 16.9, 15.0; Anal. Calcd for C10H12N2Se (239): C, 50.22; H, 5.06;
N, 11.71. Found: C, 50.20; H, 4.99; N, 11.59.
2,1,3-Benzothiadiazole (3) To a solution of commercial o-phenylenediamine (1 g, 9.25 mmol)
in dry pyridine (15 ml) was added thionyl chloride (9 ml). The mixture was refluxed for 5 h, and
then solvent was distilled off at reduced pressure. Water was added to the black residue. The
precipitate was filtered and washed with water. The crude product was chromatographed on
silica gel (AcOEt/hexane, 1:1) to give 3 as a white solid; m.p. 42-44 oC (lit. 38,40 m.p. 44 oC).
Single crystals of the reported complexes were prepared by dissolving 2,1,3-
benzochalcogenadiazole and the second crystal component in 1:1 (pfp, pfb, pfi) or 2:1 (res, tfr,
hqu, tfq, ani, cla, dib) molar ratio in appropriate solvent (see text) and slow evaporation of the
solution.
X-ray Crystallography. X-Ray diffraction data for 2β, 1·dib, 1·tfq, 1·ani were collected with
an Oxford Diffraction Xcalibur diffractometer and those for 2·pfb, 1·cla with an Oxford
Diffraction Supernova diffractometer. Data for the remaining crystals were measured with a
KM4CCD diffractometer. The crystals were mounted on a plastic loop with the use of a low-
density perfluoropolyether oil. The diffraction data were processed with the CrysAlis software.41
The crystal structures were solved by direct methods with SHELXS9742 and refined by full-
matrix least-squares with SHELXL-2014/743 within Olex-2.44 The structure of 1·I2 was
determined from a non-merohedrally twinned specimen. Drawings were prepared with Olex-244
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and Mercury45 software. Crystal data and details of data reduction and structure refinement are
given in Table 1.
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Table 1. Crystal data and refinement details.
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2α
2β
1·pfp
1423304
3·pfp
1·pfb
CCDC no.
1423307
1423308
1423311
1423302
9
Empirical formula
C6H4N2Se⋅C6H1F C6H4N2S⋅C6H1F5 C6H4N2Se⋅C7H1F
C10H12N2Se
C10H12N2Se
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5O
O
5O2
Formula weight
Crystal system
239.18
239.18
367.14
320.24
395.15
Monoclinic
130
Monoclinic
130
Monoclinic
130
Triclinic
Monoclinic
130
Temperature, K
Wavelength, Å
Space group
130
0.71073
0.71073
0.71073
0.71073
0.71073
P21/c
C2/m
P21/n
P-1
P21/c
a = 14.204(2)
b = 3.9431(9)
c = 16.645(3)
a = 17.2005(3)
b = 7.0255(1)
c = 8.4958(2)
a = 4.4075(5)
b = 10.8261(8)
c = 25.5327(16)
a = 6.7990(6)
b = 7.1071(5)
c = 13.1740(9)
α = 97.585(6)
β = 91.605(6)
γ = 107.503(7)
600.25(8)
a = 14.1550(9)
b = 6.6180(5)
c = 15.2148(13)
Unit cell dimensions, Å,°
β= 95.688(14)
β= 111.357(2)
β= 93.622(8)
β= 109.822(7)
3
927.6(3)
956.15(3)
1215.89(18)
1340.85(18)
Volume, Å
Z
4
4
4
2
4
Calculated density, g/cm3
1.713
1.662
2.006
1.772
1.957
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Absorption coefficient, mm-1
3.998
3.879
3.152
0.334
2.871
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6
8.65 to 52.74
8.46 to 52.72
8.18 to 52.74
8.56 to 52.72
8.24 to 52.74
2Θ range for data collection,°
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Reflections collected
Independent reflections
Rint, Rsigma
4507
8454
6453
6958
7704
1881
1055
2489
2442
2737
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0.0755, 0.0504
1881/0/122
1.068
0.0241, 0.0109
1055/0/83
1.156
0.0306, 0.0365
2489/0/194
1.120
0.0179, 0.0246
2442/0/190
1.062
0.0171, 0.0212
2737/0/210
1.057
Data / restraints / parameters
2
Goodness-of-fit on F
R1= 0.0578
wR2= 0.1509
R1= 0.0628
wR2= 0.1559
R1= 0.0197,
wR2= 0.0561
R1= 0.0197
wR2=0. 0.0561
0.38, -0.33
R1= 0.0448
wR2= 0.1020
R1= 0.0554
wR2= 0.1053
0.95, −0.63
R1= 0.0348
wR2= 0.0938
R1= 0.0464
wR2= 0.0979
0.39, −0.26
R1= 0.0243
wR2= 0.0579
R1= 0.0301
wR2= 0.0603
0.50, −0.47
Final R indices [I>2σ(I)]
R indices (all data)
Largest diff. peak and hole, eA-3 1.51, -1.70
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Table 1. continued
2·pfb
12·res
12·hqu
22·tfr
12·tfq
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7
CCDC no.
1423309
1423305
1423300
1423310
1423306
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Empirical formula
C10H12N2Se⋅
C7H1F5O2
451.25
(C6H4N2Se)2⋅
C6H6O2
(C6H4N2Se)2⋅
C6H6O2
(C10H12N2Se)2⋅
C6H2F4O2
660.43
(C6H4N2Se)2⋅
C6H2F4O2
548.22
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Formula weight
Crystal system
476.25
476.25
Triclinic
Triclinic
Triclinic
Triclinic
Monoclinic
130
Temperature, K
Wavelength, Å
Space group
130
130
130
130
1.54178
0.71073
0.71073
0.71073
0.71073
P-1
P-1
P-1
P-1
P21/c
Unit cell dimensions, Å
a = 7.4964(3)
b = 7.8250(3)
c = 15.3014(6)
α = 101.120(3)
β = 100.098(3)
γ = 93.800(3)
862.41(6)
a = 7.5664(7)
b = 11.1094(10)
c = 11.3805(11)
α = 104.881(8)
β = 100.371(8)
γ = 105.600(8)
858.01(15)
a = 6.7101(10)
b = 7.1434(8)
c = 9.7805(11)
α = 97.557(9)
β = 90.810(10)
γ = 112.066(12)
429.66(10)
a = 8.1807(6)
b = 10.7132(10)
c = 14.6161(11)
α = 96.887(7)
β = 94.200(6)
γ = 98.227(7)
1253.31(18)
a = 9.3870(3)
b = 5.8129(2)
c = 16.7089(5)
β = 97.489(3)
3
903.96(5)
Volume, Å
Z
2
2
1
2
2
Calculated density, g/cm3
1.738
1.843
1.841
1.750
2.014
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Crystal Growth & Design
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2
Absorption coefficient, mm-1
4.324
3.014
4.156
3
4
3.590
4.331
5
6
14.13 to 136.47
8.21 to 52.74
8.43 to 52.74
8.18 to 52.74
8.27 to 52.74
2Θ range for data collection/°
7
Reflections collected
Independent reflections
Rint, Rsigma
7839
6490
3490
13652
9648
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
3143
3487
1741
5103
1847
0.0217, 0.0216
3143/1/248
1.034
0.0175, 0.0291
3487/1/236
1.017
0.0169, 0.0228
1741/1/122
1.064
0.0391, 0.0637
5103/2/348
0.970
0.0211, 0.0172
1847/1/136
1.070
Data / restraints / parameters
2
Goodness-of-fit on F
R1=0.0334,
wR2=0.0862
R1=0.0346,
wR2=0.0875
0.70, -0.82
R1=0.0245,
wR2=0.0586
R1=0.0316,
wR2=0.0610
0.62, -0.57
R1=0.0206
wR2=0.0523
R1=0.0226
wR2=0.0530
0.47, −0.62
R1=0.0385
wR2=0.0742
R1=0.0651
wR2=0.0818
0.77, −0.54
R1=0.0179
wR2=0.0451
R1=0.0206
wR2=0.0463
0.32, −0.32
Final R indices [I>2σ(I)]
R indices (all data)
Largest diff. peak and hole, eA-3
.
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4
Table 1. continued
5
6
12·ani
1·cla
1·pfi
12·dib
1·I2
7
8
9
CCDC no.
1423297
1423298
C6H4N2Se⋅
C6H2Cl2O4
392.05
1423303
C6H4N2Se⋅
C6F5I
1423299
(C6H4N2Se)2⋅
C6F4I2
1423301
C6H4N2Se⋅I2
Empirical formula
(C6H4N2Se)2⋅
C6H4O4
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
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29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
Formula weight
Crystal system
506.24
477.03
768.00
436.87
Monoclinic
298
Monoclinic
298
Monoclinic
130
monoclinic
293
Monoclinic
293
Temperature, K
Wavelength, Å
Space group
0.71073
1.54184
0.71073
0.71073
0.71073
P21/n
C2/c
P21/n
P21/c
P21/c
Unit cell dimensions, Å
a = 4.94419(19)
b = 26.8020(13)
c = 6.8526(3)
a = 17.6480(5)
b = 8.7634(2)
c = 9.4163(3)
a = 6.9525(5)
b = 25.5310(13)
c = 15.3220(9)
a = 19.4639(7)
b = 10.8098(5)
c = 15.5794(7)
a = 4.5056(7)
b = 10.5200(17)
c = 20.541(3)
β = 93.345(4)
β = 113.834(4)
β = 100.243(5)
β = 101.574(4)
β = 94.649(13)
3
906.51(6)
1332.10(7)
2676.4(3)
3211.3(3)
970.4(3)
Volume, Å
Z
2
4
8
6
4
Calculated density, g/cm3
1.855
1.955
2.368
2.383
2.990
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Crystal Growth & Design
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Absorption coefficient, mm-1
5.164
6.386
10.173
3
4
4.113
7.695
5
6
8.40 to 52.74
13.87 to 148.99
8.26 to 52.734
8.33 to 50.05
8.71 to 50.05
2Θ range for data collection/°
7
Reflections collected
Independent reflections
Rint, Rsigma
5696
7903
14997
29091
4377
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
1847
1354
5441
5652
1611
0.0169, 0.0185
1847/1/128
1.109
0.0259, 0.0141
1354/1/96
1.097
0.0195, 0.0273
5441/0/379
1.083
0.0597, 0.0512
5652/0/407
1.026
0.0629, 0.0504
1611/78/101
1.240
Data / restraints / parameters
2
Goodness-of-fit on F
R1=0.0254,
wR2=0.0595
R1=0.0318,
wR2=0.0619
0.30, -0.28
R1=0.0308,
wR2=0.0835
R1=0.0320,
wR2=0.0850
0.33, -0.76
R1=0.0278
wR2=0.0590
R1=0.0408
wR2=0.0627
0.85, −0.71
R1=0.0394
wR2=0.0669
R1=0.0624
wR2=0.0743
0.68, −0.54
R1=0.0867
wR2=0.2689
R1=0.0925
wR2=0.2824
4.12, −2.50
Final R indices [I>2σ(I)]
R indices (all data)
Largest diff. peak and hole, eA-3
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Results and discussion
5
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8
2,1,3-Benzoselenadiazoles 1 and 2 were obtained by heating of the corresponding o-
phenylenediamines with selenium dioxide in ethanol.23-24 2,1,3-Benzothiadiazole (3) was
prepared by reaction of o-phenylenediamine with thionyl chloride in pyridine at room
temperature.46 Compound 2 was obtained in two polymorphic forms: needles 2α (m.p. 159-160
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
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58
59
60
°C; P21/c, Z’=1) grown from ethanol and needles 2β (m.p. 139-140 °C, C2/m, Z’=0.5) prepared
by evaporation from toluene. In both cases the selenadiazole molecules form centrosymmetric
dimers through the [Se–N]2 supramolecular synthon with coplanarly oriented heterocyclic units.
The Se···N distances of 2.905(3) and 2.911(2) Å in 2α and 2β, respectively, are ca. 0.2 Å
shorter than those found in the catemer structure of 1 (3.155 Å)28 and are close to the mean value
of 2.90(5) Å calculated for ten 2,1,3-benzoselenadiazole dimers found in the CSD (ver. 5.36
plus three updates).21 The N-Se···N interactions in the two polymorphs are not linear (see Table
2) but deviations of the N-Se···N angle from 180° are similar to those found in the other dimers
[the mean value 165(4)°]. The Se atom of 1,2,5-selenadiazole has a potential to form two SBIs
directed to the extensions of two Se-N bonds, however in the polymorphs of 2, analogously to
the crystal structure of 1, the chalcogen atom participates only in one short contact (Table 2). The
main difference between the two crystalline forms of 2 is in the assembly mode through aromatic
ring interactions. The dimeric units in 2α are arranged into translational stacks along the b axis
(Fig. 2a) with the interplanar distance of 3.504 Å and the distance between the centroids of the
benzene and 1,2,5-selenadiazole rings is of 3.753 Å. In contrast, the structure of 2β revealed that
the dimers, which have all their non-H atoms located on a mirror plane, aggregate in a simple
brick-wall motif parallel to (001) with the [Se–N]2 synthons located in a row just over the gap
between the dimers in the rows below and above (Fig. 2b). The closest distance between the
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centroids of the benzene rings within the brick-wall is 3.749 Å and the interplanar distance is
3.513 Å. According to the melting point values and the crystal densities, which are 1.713 g cm-3
for 2α and 1.661 g cm-3 for 2β at 130 K, the polymorph 2α is a more stable form than 2β.
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41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
Figure 2. The N-Se···N and aromatic-ring stacking interactions between the dimers of 2 in the
polymorph 2α (a) and the polymorph 2β (b). The hydrogen atoms are omitted for clarity.
Table 2. Geometry of intermolecular interactions
X-A···Y
X-A [Å]
1.793(4)
A···Y [Å]
2.905(4)
X···Y[Å] Symmetry code
1-x,2-y,-z
<X-A···Y [°]
2α
N3-Se2···N1i
168.0(1)
2β
N3-Se2···N1i
1.795(2)
2.911(2)
165.76(8)
2-x, y, 1-z
1·pfp
N1-Se2···N3i
N3-Se2···F6A
O1A-H1A···N1
1.801(4)
1.790(4)
0.80(5)
2.941(4)
3.247(3)
1.95(5)
164.3(1)
159.8(1)
160(5)
-x,1-y,1-z
2.709(5)
3·pfp
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5
6
N3-S2···F6A
1.606(2)
0.84
3.064(1)
168.78(6)
154
O1A-H1A···N1
2.00
2.777(2)
2.641(2)
2.656(3)
7
8
9
1·pfb
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51
52
53
54
55
56
57
58
59
60
N1-Se2···N3i
N3-Se2···O2A
O1A-H1A···N1
1.791(2)
1.783(2)
0.84
2.851(2)
3.127(2)
1.81
162.45(6)
163.18(6)
173
2-x,1-y,1-z
2·pfb
N1-Se2···N3i
N3-Se2···O2A
O1A-H1A···N1
1.797(2)
1.786(2)
0.84
3.021(2)
3.073(2)
1.82
163.40(8)
167.47(8)
179
1-x, 2-y, 1-z
12·res
N31-Se21···N12
N32-Se22···N11
N12-Se22···O1Ai
N11-Se21···C4Ai
O1A-H1A···N32
O2A-H2A···N31i
1.787(2)
1.783(2)
1.777(2)
1.789(2)
0.84
2.925(2)
3.262(2)
3.178(2)
3.376(2)
2.13
172.48(8)
163.14(8)
166.12(7)
164.83(8)
2.940(3)
2.809(3)
1-x, 1-y, 2-z
-1+x, y, -1+z
163
170
0.84
1.98
1-x,1-y,1-z
12·hqu
N1-Se2···O1Ai
N3-Se2···O1Ai
O1A-H1A···N1i
C7-H7···N3i
1.790(2)
1.778(2)
0.84
3.142(2)
3.278(2)
1.98
163.91(6)
158.00(6)
172
x-1, y, z
1-x,-y,1-z
2.815(2) x+1,y,z
3.431(2) x+1,y,z
0.95
2.51
163
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Crystal Growth & Design
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22·tfr
5
6
7
8
N11-Se21···N31i
N12-Se22···N32i
N31-Se21···F2A
N32-Se22···F4A
O3A-H3A···N12
O1A-H1A···N11
1.799(3)
1.795(4)
1.791(4)
1.788(4)
0.84
2.874(3)
167.3(1)
169.1(1)
169.1(1)
173.2(1)
153
2-x, 1-y, 1-z
-1-x, -y, 1-z
2.903(4)
3.048(2)
2.837(2)
2.01
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49
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57
58
59
60
2.781(5)
2.790(5)
0.84
1.98
161
12·tfq
N3-Se2···N1i
N1-Se2···F3Ai
O1A-H1A···N3
1.793(1)
1.792(1)
0.84
2.891(1)
3.122(1)
1.90
165.60(5)
161.67(5)
165
-x,-y,1-z
1-x,2-y,1-z
2.718(2)
2.781(2)
12·ani
N1-Se2···O1Ai
N3-Se2···O3Ai
O1A-H1A···N1
C7-H7···N3
C8-H8···O1i
1.782(2)
1.779(2)
0.84
3.254(2)
2.851(2)
1.95
173.06(7)
169.26(8)
168
x,y,1+z
2-x,1-y,1-z
0.93
2.54
166
3.453(3) x,y,-1+z
0.93
2.63
165
3.533(3) 2-x, 1-y, -z
1·cla
N1-Se2···O3Ai
O1A-H1A···N1
C4-H4···Cl2A
1.773(2)
0.84
3.399(2)
1.93
158.26(7)
153
0.5+x,0.5-y, -0.5+z
2.708(2)
3.607(2)
0.93
2.76
152
1·pfi
N12-Se22···N31
1.796(3)
2.972(3)
164.4 (1)
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N11-Se21···N32
C1A-I1A···N11
C1B-I1B···N12
N31-Se21···F5Bi
N32-Se22···F3Ai
1.786(3)
2.085(4)
2.077(3)
1.787(3)
1.787(3)
3.070(3)
163.1 (1)
171.2 (1)
174.8 (1)
171.4(1)
133.6(1)
3.073(3)
2.961(3)
3.289(3)
3.308(3)
0.5+x, 0.5-y, 0.5+z
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21
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52
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58
59
60
1.5-x, -0.5-y,0.5-z
12·dib
N11-Se21···N32
N12-Se22···N31
N13-Se23···N33i
C1A-I1A···N12
C1B-I1B···N13
C4A-I4A···N11i
1.790(5)
2.905 (5)
168.2 (2)
164.5 (2)
167.4 (2)
175.8 (2)
176.7 (2)
175.2 (2)
1.786 (5) 3.025 (4)
1.796 (4) 2.922 (5)
2.084 (5) 3.001 (5)
2.092 (5) 3.016 (5)
2.066 (5) 3.104 (4)
-x, 1-y, 1-z
1+x, 0.5-y, 0.5+z
1·I2
N1-Se2···N3i
I2A-I1A···N1i
I1A-I2A···Se2i
1.804 (2) 2.804 (2)
2.734 (2) 2.636 (2)
2.734 (2) 3.756 (2)
164.5 (6)
172.1 (4)
137.7 (6)
1-x, 2-y, -z
-x, -0.5+y,- 0.5-z
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Crystal Growth & Design
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40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
Figure 3. Tetrameric assemblies in 1·pfp organized into translational stacks along the a axis.
The C-bound H atoms are omitted for clarity.
Figure 4. Stacks of heterodimers in 3·pfp. The distances between the centroid of the benzene
ring of pfp and the centroids of the 1,2,5-thiadiazole and benzene rings of 3 are 3.484-3.625 Å
and 3.583-3.652 Å, respectively. The C-bound H atoms are omitted for clarity.
Diffraction quality crystals of the molecular complexes of 1 and 3 with pfp were grown from
hexane. The crystal structure of the 1:1 complex 1·pfp (P21/n, Z’=1; m.p. 83-84°C) showed that
the molecules of 1 form the [Se–N]2 dimers that bind two molecules of pfp through O–H···N
hydrogen bonds, creating centrosymmetric nearly planar four-component assemblies (Fig. 3,
Table 2). Interestingly, the Se atom forms another short contact to a fluorine substituent of the
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hydrogen-bonded pfp molecule. This N-Se···F contact has typical features of SBI: the
Se2···F6A distance of 3.247(3) Å is ca. 0.1 Å shorter than the sum of the van der Waals radii of
F and Se (3.47 Å)47 and the N-Se···F angle is 159.8(1)°. This interaction orients the pfp
molecule essentially in one plane with 1. The heterotetramers are further organized into slipped
stacks along the a axis in such a way that the aryl–perfluoroaryl interactions are excluded.
Instead, the 2,1,3-benzoselenadiazole dimers are arranged into separate translational stacks, very
similar to those in the polymorph 2α, with the centroid-centroid distance between the benzene
and 1,2,5-selenadiazole rings of 3.755 Å and the interplanar distance of 3.455 Å. The aromatic
rings of pfp molecules arranged into stacks along the b axis do not overlap but their F2A and
F5A atoms are placed directly above and below the centroids of the adjacent benzene rings, with
the centroid···F distances being of 3.209 and 3.201 Å, respectively. In contrast, the 1:1 3·pfp
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50
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53
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58
59
60
adduct (P 1 , Z’=1; m.p. 59-60°C) is composed of virtually planar heterodimers formed via O-
H···N hydrogen bond, accompanied again by N-S···F interaction (S···F distance 3.064 Å),
without any indication of the S···N SBI. This is in line with our expectations because S···N
interaction is weaker than Se···N SBI and 2,1,3-benzothiadiazoles do not form [S–N]2 dimers.
The heterodimers are further assembled into stacks along the a axis with the alternating
arrangement of the 2,1,3-benzothiadiazole and perfluorophenol molecules (Fig. 4).
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41
42
43
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45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
Figure 5. Heterotetramers formed via N-Se⋅⋅⋅N, N-Se⋅⋅⋅O and O-H⋅⋅⋅N interactions in 1·pfb and
2·pfb (left) and their packing in the crystals (right). The C-H hydrogen atoms are omitted for
clarity.
Analogously to 1·pfp, the crystals of the 1:1 complexes 1·pfb (crystallization from CH2Cl2,
m.p. 84-85°C; P21/n, Z’= 1) and 2·pfb (crystallization from n-hexane/CH2Cl2, m.p. 142-145°C;
P 1 , Z’= 1) are composed of the four-component aggregates involving the selenadiazole dimers
associated with two molecules of pfb through O–H···N hydrogen bonds and Se···O interaction
(Fig. 5). Pentafluorobenzoic acid, with the pKa value of 1.48,48 belongs to strong organic acids,
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however no proton transfer from the carboxylic group to the imine N atoms of 1 or 2 had
occurred. In both complexes the Se atoms are involved in two SBIs and the carboxylic acid
molecule binds to selenadiozole unit through the cyclic six-membered synthon involving O–
H···N and N–Se···O interactions. The geometry of the Se···X (X=N,O) contacts slightly differs
in the two structures (Table 2): in 1·pfb the Se···N contact is 0.28 Å shorter than the Se···O one
whereas in 2·pfb these two distances are similar (3.021 and 3.073 Å, respectively). Interestingly,
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even though the two complexes differ in space group symmetry, P21/c versus P 1 , their
supramolecular organization is quite similar as illustrated in Fig. 5. In both structures, the
selenadiazole dimers are arranged into a brick-wall via π-π stacking interactions. In 1·pfb the
centroid-centroid distance between the benzene and 1,2,5-selenadiazole rings is 3.589 Å and the
mean interplanar distance between the molecules of 1, that are inclined by 3.0°, is 3.273 Å. In
2·pfb distances between the analogous ring centroids are 3.601 and 3.920 Å and the interplanar
distances between strictly parallel molecules of 2 are 3.448 and 3.521 Å.
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Figure 6. (a) Hexa-component aggregate via N–Se···N, O–H··· N and π-π stacking interactions
in 12·res and (b) the (010) layer formed from these aggregates via N–Se···O and N–Se···π
interactions. The C- H hydrogen atoms are omitted for clarity.
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Since the above results confirmed our expectations concerning interaction modes of hydrogen
bond donors with selenadiazoles we tried in the next step to construct higher dimensional
aggregates using bifunctional hydrogen bond donors such as resorcinol (res) or hydroquinone
(hqu). Additionally, to explore the reliability of the cyclic synthon observed in 1·pfp involving
the O–H···N and N–Se···F interactions, perfluoroanalogues of res and hqu, 2,4,5,6-
tetrafluororesorcine (tfr) and 2,3,5,6-tetrafluorohydroquinone (tfq), were also included in this
study.
The colorless plates of the 2:1 complex 12·res (m.p. 62-63°C; P 1 , Z’=1) were obtained by a
slow evaporation from methanol. Its crystal structure revealed a centrosymmetric hexa-
component aggregate composed of two stacked dimers of 1 held together by four O–H··· N
hydrogen bonds (Fig. 6a). In this arrangement, two planar dimeric units of 1 are positioned by
the hydroxyl groups of res such that they lie stacked alongside of each resorcinol unit. This kind
of structure closely resembles those of the resorcinol cocrystals with bispyridyl derivatives
reported by MacGilivray and coworkers.49-50 All N atoms of 1 are either hydrogen bonded by the
phenolic groups or involved in the formation of dimers via [Se–N]2 synthon, therefore a second
SBI to Se atoms can only involve O atoms of the hydroxy groups or π-electrons of the aromatic
rings. In the case of Se22, a short contact is formed to the oxygen atom of res with the Se22···
O1A distance being ca. 0.1 Å shorter than the Se22··· N11 contact in the dimer (Table 2). In
turn the Se21 atom of the second symmetry independent molecule of 1 interacts additionally with
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π-electrons of the aromatic ring of res. These interactions organize the hexameric aggregates into
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(010) layer shown in Fig. 6b.
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Figure 7. Crystal structure of 12·hqu: (a) the (001) layer-type substructure generated via O–
H···N hydrogen bonds and N-Se···O interactions; (b) the (10-1) layer-type substructure
generated via N-Se···O interactions and aromatic ring interactions; (c) 3D crystal packing with
marked (001) and (10-1) substructures. The C- H hydrogen atoms are omitted for clarity.
Cocrystallization of 1 with hydroquinone (hqu) afforded 2:1 12·hqu complex (P 1 , Z’=0.5;
plates from CH2Cl2–methanol, m.p. 106-107°C) that in contrast with 12·res does not contain
selenadiazole dimers. This structure, with hqu molecule located around inversion center, is
determined not only by the expected O–H···N hydrogen bonds connecting hqu with two
molecules of 1 but also by rather weak N-Se···O SBIs of the Se atom with two hydroxy oxygen
atoms (Table 2). A cooperation between the O–H···N and N–Se···O interactions results in a
layered structure parallel to (001) shown in Fig 7a. There are two cyclic motifs within this
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structure: the eight-membered ring involving two O–H···N hydrogen bonds and two Se···O
(3.278 Å) contacts, and the four-membered ring involving two different Se···O interactions
(3.277 and 3.142 Å). In turn, a cooperation between Se···O interactions, stacking interactions
between the molecules of 1 and C-H···π interactions between the edges of 1 and faces of hqu
molecules results in another layer-type substructure parallel to (10-1) shown in Fig 7b. A
combination of these two 2D substructures leads to a characteristic 3D crystal packing (Fig. 7c)
that was previously described for 2:1 complexes of hqu with phenazine51 and quinoxaline.52
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Figure 8. Crystal structure of 22·tfr: (a) 1D supramolecular polymer created from [Se–N]2
dimers of 2 bridged by interactions with tfr; (b) aromatic-ring stacking interactions (c) crystal
packing viewed along the a axis.
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In the 2:1 complex 22·tfr (P 1 , Z’=1; prisms from CH2Cl2-n-hexane, m.p. 162-163°C) the
crystal structure is constructed from 1D supramolecular polymer created from [Se–N]2 dimers of
2 bridged by interactions with tetrafluororesorcinol (tfr). The presence of the electonegative
fluorine substituents at ortho positions to the hydroxy groups results in the formation of two
cyclic synthons based on a combination of the N–Se···F and O-H···N interactions, analogously
to those observed in 1·pfp. In contrast with res and hqu complexes, where this cyclic synthon
could not be formed, the interacting components show a nearly coplanar arrangement and form
infinite ribbons running along the [310] direction (Table 2, Fig. 8a,c). The parallel oriented
ribbons are stacked into (010) layers by π-π interactions between the benzene rings of 2 and tfr
(the ring centroids distances 3.561 and 3.680 Å) and benzene rings of 2 (the ring centroids
distance 3.784 Å) (Fig. 8b).
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Figure 9. Crystal structure of 12·tfq: (a) 1D supramolecular polymer created from [Se–N]2
dimers of 1 bridged by interactions with tfq; (b) aromatic-ring interactions (c) crystal packing
viewed along the b axis.
Essentially planar 1D polymers generated by the same set of supramolecular synthons as in
22·tfr are also found in the structure of the 2:1 complex 12·tfq (P21/c, Z’=0.5; yellow prisms
from CH2Cl2–heptane with a drop of MeOH, m.p. 150–151 oC; see Table 2 and Fig. 9a). Owing
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