Synthetic, structural, and computational investigations of N-alkyl benzo-2,1,3-selenadiazolium iodides and their supramolecular aggregates

Article abstract of DOI:10.1039/c5dt04314j

Despite their versatility, the application of telluradiazoles as supramolecular building blocks is considerably constrained by their sensitivity to moisture. Albeit more robust, their selenium analogues form weaker supramolecular interactions. These, however, are enhanced when one nitrogen atom is bonded to an alkyl group. Here we investigate general methods for the synthesis of such derivatives. Methyl, iso-propyl and tert-butyl benzo-2,1,3-selenadiazolium cations were prepared by direct alkylation or cyclo-condensation of the alkyl-phenylenediamine with selenous acid. While the former reaction only proceeds with the primary and tertiary alkyl iodides, the latter is very efficient. Difficulties reported in earlier literature are attributable to the formation of adducts of benzoselenadiazole with its alkylated cations and side reactions initiated by aerobic oxidation of iodide. However, the cations themselves are resilient to oxidation and stable in acidic to neutral aqueous medium. X-ray crystallography was used in the identification and characterization of the following compounds: [C₆H₄N₂(R)Se]⁺X^-, (R = CH(CH₃)₂, C(CH₃)₃; X = I^-, I₃^-], [C₆H₄N₂(CH₃)Se]⁺I^-, and [C₆H₄N₂Se][C₆H₄N₂(CH₃)Se]₂I₂. Formation of Se?N secondary bonding interactions (chalcogen bonds) was only observed in the last structure as anion binding to selenium is a strong competitor. The relative strengths of those forces and the structural preferences they enforce were assessed with DFT-D3 calculations supplemented by AIM analysis of the electron density.

Full text of DOI:10.1039/c5dt04314j

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ARTICLE
Synthetic, Structural, and Computational Investigations of N-
alkyl Benzo-2,1,3-Selenadiazolium Iodides and their
Supramolecular Aggregates
Received 00th January 20xx,
Accepted 00th January 20xx
Lucia M. Lee,a Victoria B. Corless,a Michael Tran,a Hilary Jenkins,a James F. Brittena and
DOI: 10.1039/x0xx00000x
Ignacio VargasꢀBacaa*
www.rsc.org/
Despite their versatility, the application of telluradiazoles as supramolecular building blocks is considerably constrained by
their sensitivity to moisture. Albeit more robust, their selenium analogues form weaker supramolecular interactions. These,
however, are enhanced when one nitrogen atom is bonded to an alkyl group. Here we investigate general methods for the
synthesis of such derivatives. Methyl, isoꢀpropyl and tertꢀbutyl benzoꢀ2,1,3ꢀselenadiazolium cations were prepared by direct
alkylation or cycloꢀcondensation of the alkylꢀphenylenediamine with selenous acid. While the former reaction only proceeds
with the primary and tertiary alkyl iodides, the latter is very efficient. Difficulties reported in earlier literature are
attributable to the formation of adducts of benzoselenadiazole with its alkylated cations and side reactions initiated by
aerobic oxidation of iodide. However, the cations themselves are resilient to oxidation and stable in acidic to neutral
aqueous medium. Xꢀray crystallography was used in the identification and characterization of the following compounds:
ꢀ
[C6H4N2(R)Se]+Xꢀ, (R = CH(CH3)2, C(CH3)3; X = Iꢀ, I3 ], [C6H4N2(CH3)Se]+Iꢀ, and [C6H4N2Se][C6H4N2(CH3)Se]2I2.
Formation of Se…N secondary bonding interactions (chalcogen bonds) was only observed in the last structure as anion
binding to selenium is a strong competitor. The relative strengths of those forces and the structural preferences they enforce
were assessed with DFTꢀD3 calculations supplemented by AIM analysis of the electron density.
applications. In addition to the selfꢀassociation of 1,2,5ꢀ
telluradiazoles through Te…N interactions, other studies have
also evaluated their affinity to Lewis bases in both solid10 and
solution.11ꢀ13 In spite of their versatility, prospects of
widespread application of telluradiazoles are limited by their
sensitivity to moisture.
Introduction
While hydrogen bonding and the coordination of metal ions are
preponderant in supramolecular chemistry, other interactions
are receiving increasing interest in this field. A notable example
is halogen bonding,1ꢀ3 a special case of the phenomenon termed
secondary bonding4 that is recurrent in the structures of
compounds of the heavy pꢀblock elements. The potential of
secondary bonding in supramolecular chemistry is well
exemplified by the derivatives of the 1,2,5ꢀtelluradiazole ring
(1, Chart1). Their molecules usually associate by two
antiparallel Te…N secondary bonding interactions forming the
[TeꢀN]2 supramolecular synthon,5 a virtual fourꢀmembered ring
(Scheme 1, E = Te).6 In the absence of substantial steric
hindrance, each molecule can simultaneously form the [TeꢀN]2
supramolecular synthon twice building in this way
supramolecular ribbons.7 The driving force for association of
these molecules is strong enough to overcome moderate steric
repulsion by allowing structural distortion of the ribbons. This
effect induces properties such as chromotropism8 and secondꢀ
harmonic generation9 which are of interest for practical
Chart 1
Scheme 1
The lighter members of the chalcogenadiazole family (2,3
,
Chart 1) are much more robust but SBIs centred on S and Se
atoms are weaker than those formed by Te14 and instances of
supramolecular association are less frequent in such cases.
However, crystallographic evidence suggests that attachment of
Lewis acid (a transition metal ion15,16 or a borane17), on one
nitrogen of the heterocycle strengthens the secondary
interactions made by Se and Te, shortening the corresponding
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distances. Such effect is also strong in the cations formed by Nꢀ amines with 1ꢀfluoroꢀ2ꢀnitrobenzene, followed by reduction
alkylation and provides an explanation for the peculiar trend in with H2 catalyzed by Pd/C.24ꢀ26 Benzoꢀ2,1,3ꢀselenadiazole was
reduction
potentials
of
the
Nꢀmethylꢀbenzoꢀ2,1,3ꢀ prepared by the reaction of 1,2ꢀphenylenediamine with
chalcogenadiazolium cations in acetonitrile.18 Such evidence of selenium dioxide according to literature.27 Anhydrousꢀgrade
molecular association in solution through SBIs is consistent solvents were used without further purification.
with the observation of [M2H]+ supramolecular aggregates in Instrumentation. 1H, 13C and 77Se NMR spectra were recorded
the mass spectrum of benzoꢀ2,1,3ꢀtelluradiazoles19 as well as on Bruker 200 and Bruker 600 spectrometers at ambient
calculated interaction energies and AIM parameters.12,18
temperature. Chemical shifts are reported in δ values (parts per
Nꢀalkyl substituted selenadiazolium cationic rings could million) with respect to the resonances of tetramethylsilane for
therefore be a convenient alternative to telluradiazoles in 1H and 13C and with respect to the line of Me2Se for the
supramolecular architecture, provided that they are reasonably chemical shift of 77Se. In the last case, spectra were obtained
1
stable and the preparation methods are flexible enough to using Hꢀ77Se HMBC unless otherwise stated. IR spectra were
accommodate multiple variations in the structure. The most recorded on polyethylene pellets on a Nicolet 6700 FTꢀIR
straightforward synthetic method would be the direct alkylation spectrometer with a resolution of 4 cmꢀ1. Raman spectra were
of the heterocycle in
4 (Chart 2). However, early reports of this obtained with a Renishaw inVia spectrometer exciting at 785
approach describe very inefficient reactions plagued by nm, 30 mW, averaging 10 x 10s scans. Lowꢀ and highꢀ
multiple byꢀproducts with most common alkylating resolution electrospray spectral analyses were performed using
reagents.20,21 Clean and efficient alkylations have been reported Micromass GCT spectrometer and a Micromass Quattro Ultima
rather recently using very reactive agents such as MeꢀOS(O)2ꢀ for electron ionization spectra. In each case, the sample was
18
R’ (R’
=
OMe, C6H2(NO2)2ꢀ2,4),20 F3CꢀSO3ꢀCH3
or introduced into the ionization chamber in a shortened
(CH3)3O+BF4ꢀ22; but these methods are applicable with only a borosilicate glass capillary on a probe rod. The samples were
handful of alkyl groups. Alternatively, the alkyl group could be then heated and the temperature range that displayed the most
attached to nitrogen before formation of the heterocycle. This intense parent ion peaks was used for spectral acquisition. A 70
approach was actually reported in an early publication20,21 but eV electron stream ionized the sample and the positively
its products were not structurally authenticated. A third route to charged ions were identified by a timeꢀofꢀflight detector. A
Nꢀalkyl selenadiazolium cations, also limited in flexibility, Cary 50 UVꢀvis spectrometer and its Cary WinꢀUV software
consists of the spontaneous deꢀalkylation of one N nitrogen package were used to acquire the spectra. Additional processing
atom during the reaction of N,N’ꢀbis(tertꢀbutyl)ꢀdiazabutadiene was carried out using the GramsAI suite (version 8.0). Melting
with SeCl4.23
points were measured on a ThomasꢀHoover melting point
apparatus and are reported uncorrected. Elemental analysis was
performed by the Science Centre of London Metropolitan
University, 29 Hornsey Road, London, UK, N7 7DD.
All single crystal Xꢀray diffraction samples were mounted with
paratone oil at the tip of a glass fibre installed on a MiTeGen
goniometer head, and kept under a cold stream of nitrogen
while on the diffractometer. Data were collected at 100 K on a
Bruker APEX2 diffractometer, using Mo K α radiation (λ =
0.71073 Å) and outfitted with an Oxford cryostream lowꢀ
temperature accessory. ꢁ and ϕ scans were collected in 0.5°
steps with a crystal to detector distance of 4.954 cm. The
preliminary unit cell parameters were determined using a
minimum of 50 frames from three different orientations, and
final cell refinement after integration in SAINT. Data were
corrected for absorption and scaled using faceꢀindices as well
as redundant data in SADABS. Crystal structures were solved
using SHELXL and most structures were refined by fullꢀmatrix
least square of all F2 values with the WinGX package.
Chart 2
As we are interested in using the Nꢀalkylated selenadiazolium
cations as supramolecular building blocks, in this report we
compare the two most flexible synthetic methods for the
preparation of the derivatives with primary, secondary and
tertiary alkyl groups (5, Chart 2). We examine the crystal
structures of their iodide salts, the affinity of the cations for
halide anions, and spectroscopic properties useful for the
characterization of these species in solution.
Syntheses
(C6H4N2Se)[C6H4N(NCH3)Se]2[I]2 (4[5a]2[I]2). Benzoꢀ2,1,3ꢀ
selenadiazole (0.1 g, 0.547 mol) and neat iodomethane (0.35
mL, 0.602 mmol) were mixed with stirring under nitrogen. The
mixture became purple and gave a microcrystalline red powder.
Yield 60%. The product was washed with hexanes and dried
under vacuum. Crystals suitable for single Xꢀray diffraction
were grown by slow diffusion of the reagents dissolved in
Experimental
Materials and General Procedures. Selenium dioxide,
iodomethane were used as received from commercial suppliers.
The Nꢀalkyl 1,2ꢀphenylenediamines were prepared from the
reaction of the corresponding commerically available primary
1
ethanol. H NMR (d6ꢀDMSO, 600 MHz): δ 4.13 (s, 3H, CH3),
2 | J. Name., 2012, 00, 1ꢀ3
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7.54, 7.82, 7.96 (m, 6H, ArꢀCH) ppm. 13C NMR (d6ꢀDMSO, DMSO, 600 MHz): δ 158.46 148.03 (ArꢀC) 136.44 (ArꢀC)
600 MHz): δ 159.74 156.40 150.622 131.65 126.43 125.88 129.51 (ArꢀC) 126.17 (ArꢀC) 118.40 (ArꢀC) 67.28 (NꢀCH)
116.91 (ArꢀCH) 39.42 (CH3) ppm. 77Se NMR (d6ꢀDMSO, 600 29.66 (CH3)3 ppm. 77Se NMR (d6ꢀDMSO, 600MHz): δ 1454.7
MHz): δ 1494.0 ([C6H4N(NCH3)Se]+), 1529.7 (C6H4N2Se) ppm. LR ESIꢀMS: m/z 241.0 (M+) HR ESIꢀMS: m/z 241.0248
ppm. IR (cmꢀ1): 3602 (m), 2854(b), 2341 (m), 2150 (vw), 2018 (M+) (cf. calc. for C10H13N2Se 241.0244). IR (cmꢀ1) 3647 (vw),
(w), 1982 (w), 1949 (w), 1812 (w), 1600 (w), 1529 (m), 1515 3604 (w), 2793 (b), 2340 (w), 2150 (vw), 2108 (w), 1859 (vw),
(m), 1464(sh), 1134 (vw), 1044(m), 905(vw), 730 (sh) 720 (sh). 1602 (w), 1526 (w), 1472 (sh), 1371 (m), 1302 (m), 1180 (w),
Mp. 148–150 °C (d). E.A. % calcd. for C20H18I2N6Se3: C 28.83, 1132 (w), 954 (vw), 872 (vw), 844 (vw), 744(sh), 719 (sh).
H 2.18, N 10.09, ; found C 28.72, H 2.09, N 9.98.
C6H4N(NCH3)Se][I] ([5a][I]). Method A. A sample of 132 °C (d).
5a]2[I]2 (0.02 g, 0.109 mmol) was dissolved in methanol (1.6 Computational Methods. All the structures considered in this
UVꢀVis λmax = 330 nm, ε=282.5 L molꢀ1cmꢀ3. Mp. 130–
[
4[
mL) with stirring at 42ꢀ46 °C. The colour of the solution slowly study were fully optimized using the ADF DFT package
changed from dark green to bright red. Cooling to room (versions 2013.01ꢀ20140.1).28,29 The Adiabatic Local Density
temperature produced red crystals which were recovered by Approximation (ALDA) was used for the exchangeꢀcorrelation
filtration. Yield 17%. Method B. To a solution of Nꢀmethylꢀ kernel30,31 and the differentiated static LDA expression was
phenylenediamine (0.11 mL, 1.023 mmol) and H2SeO3 (0.1319 used with the VoskoꢀWilkꢀNusair parameterization.32,33
g, 1.023 mmol) in anhydrous ethanol, trifluoroacetic acid (0.07 Calculation of model geometries was gradientꢀcorrected with
mL, 1.023 mmol) was added dropwise under nitrogen. The the exchange and correlation functionals of Perdew, Burke and
reaction mixture was allowed to stir at room temperature for 20 Ernzerhof (PBE)34 and applying the zerothꢀorder regular
min, time after which a solution of NaI (0.1533 g, 1.023 mmol) approximation (ZORA)34ꢀ38 formalism with the specially
in ethanol (10 mL) was added with vigorous stirring, a dark red adapted tripleꢀζ allꢀelectron plus oneꢀpolarizationꢀfunction basis
solid precipitate formed and was separated by filtration, washed sets. The contribution of dispersion was modelled with
with hexanes, dried under vacuum and stored under nitrogen. Grimme’s correction.39 Analytical frequency calculations were
Yield 22%. 1H NMR (D2O, 600MHz): δ 4.60 (s, 3H, CH3), performed to ensure that each geometry was at an energy
7.78, 7.96 (m, 4H, ArꢀCH) ppm. 13C NMR (d6ꢀDMSO, 600 minimum.40,41 The TDꢀDFT calculation was performed from
MHz): δ 156.36, 150.73, 136.53, 129.95, 125.02, 116.46 (Arꢀ the optimized geometry of [C6H4N(NCH3)Se]+ using the
C), 38.35 (CH3) ppm. 77Se NMR (d6ꢀDMSO, 600MHz): δ statistical average of potentials model for exchange and
1490.4 ppm. LR ESIꢀMS: m/z 199.0 (M+). HR ESIꢀMS: m/z correlation (SAOP)42ꢀ44 and a basis set of quadrupleꢀzeta quality
198.9774 (M+) (cf. calc. for C7H7N2Se 198.9774). IR (cmꢀ1): plus polarization.
3606 (m), 3219 (w), 2913 (s), 2866 (b), 2345 (m), 2018 (w),
1956 (w), 1811(w), 1536 (w), 1470 (m), 1305 (w), 1167 (vw),
Results and discussion
1135(m), 807 (w), 744(sh), 730(sh), 720 (sh). UVꢀVis λmax
345 nm,
= 664.6 L molꢀ1cmꢀ3. Mp. 184ꢀ188 °C (d).
=
ε
Syntheses by direct alkylation. Although benzoꢀ2,1,3ꢀ
selenadiazole is a weak base, it is readily protonated by strong
acids.45 For this reason, the purported inefficiency20,21 of its
reaction with primary alkylꢀiodides is unusual and merited
reinvestigation using a more reactive tertiary iodide. Initial
attempts at benchꢀtop alkylation with (CH3)3CI in a hot toluene
[C6H4N(NCH(CH3)2)Se]2[I] ([5b][I]). To a solution of Nꢀ
isopropylꢀbenzeneꢀ1,2ꢀdiamine and H2SeO3 in anhydrous
ethanol, trifluoroacetic acid was added. The reaction mixture
was allowed to stir at room temperature for 20 min under
nitrogen. Upon the addition of NaI, the product immediately
precipitated. The dark red solid was washed with hexane, dried
1
solution yielded a complex mixture, as made evident by the H
1
and stored under a nitrogen atmosphere. Yield 30%. H NMR
NMR spectrum. Slow evaporation of the solution yielded a
mixture of crystals with multiple morphologies; three of which
were identified by singleꢀcrystal Xꢀray diffraction: [5c][I3],
(CD2Cl2, 600 MHz): δ 7.99 (dd, 1H, J= 6, 12Hz, ArꢀCH) 5.60
(sept, J= 6Hz, 1H, NHꢀCH) 1.87 (d, 6H, J= 7 Hz, CH3) ppm.
13C NMR (CD2Cl2, 600 MHz): δ 138.18 (ArꢀC), 131.42 (ArꢀC),
125.34 (ArꢀC), 115.71 (ArꢀC) 57.87 (NHꢀCH), 24.22 (CH3)
ppm. 77Se NMR (d6ꢀDMSO, 600MHz): δ 1459.5 ppm. LR ESIꢀ
MS: m/z 227.0 (M+). HR ESIꢀMS: m/z 227.0095 (M+) (cf. calc.
for C9H11N2Se 227.0088). IR (cmꢀ1): 3605 (w), 3374 (m), 2848
(b), 2329 (w), 2010 (vw), 1952 (w) 1980 (vw), 1842 (vw), 1896
(vw), 1809 (vw), 1720 (vw), 1523 (w), 1473 (sh), 1369 (m),
1314 (m), 1176 (sh), 1164 (sh), 1142 (m), 1121 (m), 823 (w),
[
4
]2[
does contain the Nꢀtertꢀbutyl benzoꢀselenadiazolium cation
5c), which demonstrates that the alkylation reaction does
4ꢀH]2[I][I3] and [4
]2(C6H4(NH2)2H+)2][I]2. The first species
(
proceed. However, the presence of the triiodide anion, plus
protonated phenylenediamine and benzoselenadiazole point to
the actual problem with this experiment: the iodide ion is likely
oxidized by atmospheric oxygen to I3 which then halogenates
the solvent or benzoselenadiazole to generate HI. Crystals of
ꢀ
757 (vs), 730 (vs), 719 (vs). UVꢀVis λmax = 343 nm,
428.5 L molꢀ1cmꢀ3. Mp. 165ꢀ168 °C (d).
ε =
[
5c][I] were obtained when the reaction was carried out under
an atmosphere of nitrogen, albeit in low yield. Similarly, the
alkylation reaction proceeded with neat CH3I in anaerobic
conditions, however, in this case the alkylation is incomplete
[C6H4N(NC(CH3)3)Se][I] ([5c][I]). Using the procedure above
described for [5a][I] and [5b][I], the compound was obtained as
1
a dark red crystalline material. H NMR (d6ꢀDMSO, 600MHz):
due to the formation of the crystalline
4[5a]2[I]2, which was
δ 8.30(d, 1H, ArꢀCH) 8.08(d, 1H, ArꢀCH) 7.97 (dd, 1H, Arꢀ
CH) 7.79 (dd, 1H, ArꢀCH) 1.97 (9H, (CH3)3). 13C NMR (d6ꢀ
identified by Xꢀray diffraction. The salt [5a][I] was obtained
from
4
[
5a]2[I]2 by recrystallization from dilute solutions.
J. Name., 2013, 00, 1ꢀ3 | 3
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Interestingly, isoꢀpropyl iodide was completely unreactive as expected but we found more convenient to carry out the
towards benzoselenadiazole under the same conditions. While reaction in a mixture of ethanol and trifluoroacetic acid in order
the reaction of tertꢀbutyl iodide is likely to proceed by a SN1 to avoid using the less volatile acetic acid. Structural
mechanism, it is likely that the primary and secondary iodides characterization by Xꢀray diffraction did confirm the identity of
prefer a SN2 mechanism but steric hindrance prevents the the products. We also found that exposure of the cations in
reaction of the isoꢀpropyl halide.
solution to the atmosphere resulted in iodide oxidation and
Condensation of selenous acid with N-alkylated crystallization of the corresponding triiodide salts, which was
phenylenediamines.
Even
in
aqueous
medium, verified by the strong scattering band at 111 cmꢀ1 in the Raman
benzoselenadiazole is readily formed by the reaction of H2SeO3 spectrum48 or crystallographic analysis.
and phenylenediamine. Nꢀsubstituted orthoꢀdiamino benzenes X-ray crystallography. Crystallographic and refinement data
were reported to undergo an analogous reaction in glacial acetic for the salts of the three cations are presented in Table 1;
producing the benzoselenadiazolium cations, which are isolated selected distances and angles in each crystal structure are
by precipitation with sodium halide.46,47 This procedure works provided in Table 2.
Table 1. – Crystallographic and Refinement Parameters for 4[5a]2[I]2 and the salts of 5a-c.
4[5a]2[I]2
[
5a][I]
[5b][I3]
[5b][I]
[
5c][I3]
[5c][I]
Chemical formula
C20H18I2N6Se3
1424372
833.08
C7H10N2SeI
1424371
325.01
C9H11N2SeI3
1424373
606.86
C9H11N2SeI
1424374
353.06
C10H13N2SeI3
1424370
620.9
C10H13N2SeI
1434655
367.08
CCDC
Formula mass
Crystal system
monoclinic
15.986(1)
11.671(1)
12.743 (1)
90
monoclinic
6.471(1)
13.216(2)
10.474(2)
90
monoclinic
11.317(2)
9.818(2)
13.569(2)
90
monoclinic
16.084(1)
10.525(1)
6.597(1)
90
monoclinic
7.668(1)
10.014(2)
20.949(4)
90
orthorhombic
11.668(1)
7.699 (1)
13.253 (1)
90
a,Å
b,Å
c,Å
α,°
b,°
92.566(3)
90
92.426(4)
90
105.047(3)
90
90
95.631(3)
90
90
γ,°
90
90
Unit cell volume, Å3
Temperature, K
Space group
2375.2(2)
100.15
894.9(3)
100.15
1456.0(4)
100.15
1116.8(2)
100.15
1600.7(5)
100.15
1190.6(1)
296
C 1 2/c1
P 21/n
P 1 21/n 1
P n a 21
P 21/c
P n m a
Z
4
4
4
4
4
4
No. of reflections measured
2700
12698
19082
16547
8761
26960
No. independent reflections
2213
2521
4908
3306
4094
3066
Final R1 values (I > 2σ(I))
0.0404
0.0685
0.0199
0.0385
0.0261
0.0447
0.0229
0.0419
0.0381
0.0759
0.0331
0.0828
Final wR(F2) values (I > 2σ(I))
Final R1 values (all data)
0.0550
0.0733
0.0262
0.0404
0.0399
0.0481
0.0276
0.0434
0.0682
0.0861
0.0413
0.0847
Final wR(F2) values (all data)
ꢖ
ꢗ/ꢖ
ꢕ
ꢊ
∑
|ꢁ −ꢁ
ꢂꢃꢄ
| and ꢈꢀ ꢁ2
=
∑
ꢉ
ꢌ
ꢋ ꢍ
ꢑꢍ
ꢅꢆꢇꢅ
|
ꢎꢏꢐ
ꢒꢓꢔꢒ
ꢖ
ꢉ
ꢊ
ꢀ1
=
∑
ꢋꢍ
∑
|ꢁ
ꢂꢃꢄ
ꢎꢏꢐ
The crystal structure of
4
[
5a]2[I]2 consists of a molecule of
4
the molecules of4 and 5a are nearly coplanar with a deviation
bound to two 5a, conforming a pseudoꢀtrimer assembled by two angle of 5.06°. This structure also features SeꢀI short distances
asymmetric [SeꢀN]2 supramolecular synthons (Figure 1) with
asymmetric SBI distances of 2.576(1) and 2.934(1) Å. This
aggregate is analogous to the product formed by the reaction of
benzoselenadiazole with [(CH3)3O][BF4]22, in which the Se…N
and Se…F secondary bonding distances are 2.573(2) and
2.966(6) Å and 2.970(4) Å respectively. In this arrangement,
at 3.528(1) Å and 3.831(1) Å. Both iodides sit out of the
average plane of the aggregate forming a virtual fourꢀ
membered ring (i.e. the [Se I]2 supramolecular synthon) with
the Se atoms of the 5a molecules of two neighbouring
pseudotrimers.
4 | J. Name., 2012, 00, 1ꢀ3
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Table 2. Selected Bond Distances and Angles for 4[5a]2[I]2 and the salts of 5a-c.
Compound
SeꢀN1
4
[
5a]2[I]2
[
5a][I]
5b[I3]
[
5b][I]
[
5b][I3]
5c.I
1.856(5)
1.777(5)
1.339(7)
1.336(7)
1.443(7)
1.432(8)
1.366(8)
1.428(8)
1.371(8)
1.428(8)
88.7(2)
1.785(2)
1.875(2)
1.327(3)
1.329(3)
1.440(3)
1.431(3)
1.351(4)
1.431(4)
1.359(3)
1.422(3)
88.16(9)
111.2(2)
111.4(1)
124.9(2)
123.7(2)s
1.766(3)
1.857(3)
1.333(4)
1.338(4)
1.444(4)
1.355(5)
1.426(5)
1.426(5)
1.353(4)
1.422(5)
89.6(1)
1.774(3)
1.881(2)
1.333(4)
1.338(4)
1.439(4)
1.428(6)
1.355(6)
1.360(4)
1.427(5)
1.425(5)
88.6(2)
1.742(5)
1.841(4)
1.349(8)
1.347(6)
1.414(7)
1.414(7)
1.342(9)
1.400(9)
1.345(9)
1.418(1)
90.4(4)
1.749(2)
1.864(2)
1.343(3)
1.339(3)
1.442(4)
1.421(4)
1.361(3)
1.417(4)
1.368(4)
1.421(3)
90.2(1)
SeꢀN2
N1ꢀC1
N2ꢀC6
C1ꢀC6
C1ꢀC2
C2ꢀC3
C3ꢀC4
C4ꢀC5
C5ꢀC6
N1ꢀSeꢀN2
SeꢀN1ꢀC1
SeꢀN2ꢀC6
SeꢀN2ꢀC7
C6ꢀN2ꢀC7
111.3(4)
111.6(4)
124.0(4)
124.4(5)
110.7(2)
110.6(2)
124.4(2)
125.1(3)
111.0(3)
111.0(3)
124.7(3)
124.3(3)
109.7(7)
109.8(7)
122.4(6)
127.8(8)
110.3(2)
110.2(2)
122.4(2)
127.5(2)
Figure 2. Crystal structures of (a) [5b][I3] and (b) [5c][I3]. Selected bond distances
(a) Se…I1: 3.249(1) Å, Se…I2: 3.626(5) Å; (b) Se…I1: 3.309(1) Å, Se…I2: 3.727(1) Å.
Figure 1. Arrangements of molecules and ions in the crystal
distances: Se1…N1: 2.573(4) Å and 2.5937 Å.
4[5a]2[I]2. Selected
The arrangement of the ions and the Se…I interactions in the
In clear contrast with the structures of the pseudoꢀtrimers,22 and
the dimers observed for and
5a][CF3SO3]18
[C2H2N(NC(CH3)3)Se][GaCl4]49, the crystal structures of the
iodide and triiodide salts of the alkylated cations 5a-c feature
no association of the heterocycles to each other. In all cases,
strong Seꢀanion interactions prevent formation of the Se…N
SBIs (Figures 2 and 3).
The triiodide anions in the crystals of [5b][I3] and [5c][I3]
engage in two interactions with the selenium atom. The shortest
(3.249(1), 3.309(1) Å, respectively) is with the terminal iodine
atom I1; the contact to the middle I2 atom is longer (3.626(1),
3.727(1) Å, respectively), cf. the sum of van der Waals radii
3.88 Å. In the case of [5b][I3] the terminal iodine atom I3 is in
close proximity (3.491(3) Å, cf. the sum of van der Waals radii
3.53 Å) to the nitrogen atom of a neighbouring 5b cation, the
nearly linear geometry of this arrangement is indicative of a
halogen bond. Consequently, the I2ꢀI3 bond is longer (2.879(1)
Å) in [5b][I3] than in [5c][I3] (2.829(1)]
[
5a-c][I] lattices are influenced the size of the alkyl group
] confines the Se…I
[
(Figure 3). The small methyl group in [5a][
I
interactions to the plane of the cation forming iodideꢀbridged
dimers that conform the [Se I]2 supramolecular synthon with
short (3.178 (1) Å) and long (3.610 (1) Å) SBIs. Similar
binding of anions to Se has been observed in related species.
For example, a virtual fourꢀmembered ring consisting of Se and
Cl atoms is formed in the crystal structure of
[C2H2NN(H)Se][Cl] (2.900(1) Å and (3.075 (1) Å).45 The
structure of [C2H2N(NC(CH3)3)Se][Cl] also features a planar
selenadiazole ring with one SeꢀCl bond distance of 2.605 (1)
–
Å.23 In contrast, the GaCl4 salt of the same selenadiazole
heterocycle does not display any SeꢀCl short interactions,
instead it contains the [SeꢀN]2 supramolecular synthon.23 The
larger alkyl groups favour interlayer interactions (eminently
electrostatic) in [Se I]∞ supramolecular chains. The SeꢀI
distances are 3.043 (1) Å and 3.696 (1) Å in the structure of
[
5b][I] and 3.147 (1) and 3.880 (1) Å in [5c][I].
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salts. For computational expediency, GGA calculations were
performed with the PBE functional, supplemented by
dispersion and relativistic corrections. Model structures were
optimized from the crystallographic coordinates and expanded
to include hypothetical isomers and the analogues with chloride
and bromide anions. Whenever an experimental structure was
available, bond lengths were reproduced within 0.01 Å, the
largest deviations correspond to the intramolecular SeꢀN
distances. Seleniumꢀcentred secondary bond distances were
reproduced within 0.01 Å to nitrogen and 0.50 Å to iodide. The
large deviation in the latter case is likely due to the additional
interactions of the anion in the lattices. Interaction energies
were evaluated using the transitionꢀstate method50 that
partitions the energy of interaction between two molecules or
fragments in a hypothetical process in which the constituting
units are first calculated individually, brought to their
equilibrium positions without orbital mixing, and finally the
electron density is relaxed by the interaction of fragment
orbitals. The change from the first to the second step is
regarded as the total steric interaction that results from the sum
of the electrostatic (EElstat) and Pauliꢀrepulsion (EPauli). The third
step gives the orbital interaction energy (EOrb). Dispersion is
treated as a separate contribution (EDisp). The total interaction
energy is given by the sum of all contributions (Eq. 1).
Figure 3. Packing arrangement in the crystal structures of the iodide salts of
(a) 5a (b) 5b and (c) 5c
.
Spectroscopy in solution. The iodide salts of 5a-c are stable in
air. The compounds are slightly soluble in water at room
temperature, their solubility decreases with the size of the R
group. In fact, it is possible to recrystallize 5a from hot water.
Aqueous solutions of the cations have a characteristic redꢀ
brown colour, their UVꢀvis absorption spectrum displays
prominent maxima in the range of 330 ꢀ 343 nm and a weaker
band between 440 ꢀ 460 nm. These spectra are in excellent
agreement with the TDꢀDFT calculation for the 5a, which
EInteraction = EElstat +EPauli + EOrb + EDisp
(1)
attributes the bands to the LUMO
← HOMO and
LUMO HOMOꢀ1 excitations (Figure 4). The UVꢀvis spectra
←
do not change from neutral to acidic pH, but hydrolysis ensues
in basic medium. Given the modest solubility of the 5a-c
iodides, their 77Se NMR chemical shifts are best obtained
through 1Hꢀ77Se heteronuclear multiple bond correlation
(HMBC) experiments. The 77Se
δ values (1455ꢀ1490 ppm)
appear at slightly lower frequency than the 1515 ppm reported
for [C6H4N(NCH3)Se][CF3SO3] in acetonitrile.18 For the
pseudoꢀtrimer 4[5a]2[I]2, two resonances were observed with
frequencies that correspond to those of the constituting neutral
and cationic molecules, suggesting that the aggregate
dissociates in solution.
Figure 5. Partition schemes used in the DFT-D3 fragment interaction analyses. Each
fragment (region) is identified with a distinct colour.
Figure 4. Experimental (left) and calculated (right) UV-vis spectra of [5a][I].
Three partitioning schemes (Figure 5, iꢀiii) were used to
evaluate the secondary interactions within the pseudoꢀtrimer
Frontier orbitals shown as an inset in the calculated spectrum.
4[5a]2[I]2 the results are summarized in Table 3. In this analysis
DFT calculations. As the crystal structures show there is
competition between the formation of the [SeꢀN]2
supramolecular synthon and binding of the anion to selenium,
the relative strengths of these interactions were evaluated using
DFT and were extended to include the chloride and bromide
the average interaction energy of the [SeꢀN]2 supramolecular
synthon was 56.4 kJ/mol. Formation of the interactions in iii
and ii could be regarded as steps in the assembly of the
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pseudotrimer and the calculations show that the interaction distances. In order to assess the relative strength of each SBI, a
energies are nearly additive.
bondꢀenergy decomposition analysis was performed using the
extended-transition-state method from the natural orbitals for
chemical valence (ETSꢀNOCV)51. In this method the orbital
component to the total bonding energy between fragments is
calculated as in Eq. 2.
Table 3. Contributions to the energies (kJ/mol) of fragment interaction in 4[5a]2[I]2
calculated under partition schemes iꢀiii.
Partition
EInt
EElstat
EPauli
EOrb
EDisp
Scheme
ꢡ/ꢢ
i
ꢀ112.05
ꢀ55.54
ꢀ57.65
ꢀ294.18
ꢀ145.38
ꢀ147.58
416.15
209.63
208.39
ꢀ203.76
ꢀ102.26
ꢀ103.30
ꢀ30.26
ꢀ17.54
ꢀ15.16
ꢟꢠ
ꢝ ∆ꢘꢜꢝꢚꢛ
=
ꢞꢝꢌ−ꢁꢑꢟꢝꢠ,ꢑꢝ + −ꢁ
ꢕ
(2)
∑
∑
ꢝꢣꢤ
∆ꢘꢙꢚꢛ
=
ꢝ,ꢝ
ii
iii
ꢟꢠ
The terms −ꢁ
are diagonal transitionꢀstate KohnꢀSham
ꢑꢝ,ꢝ
matrix elements corresponding to NOCV’s with eigenvalues
−ꢞꢝ and ꢞꢝ respectively. This particular orbital interaction term
provides both a qualitative and quantitative picture of the
electronic density reorganization in the [SeꢀN]2 supramolecular
synthons. Each of the fragment interaction calculations (iꢀiii)
shows that the shorter Se…N SBI, that opposite to the
quaternary nitrogen, is stronger (ꢀ13.0 to ꢀ16.9 kcal/mol) than
the longer (ꢀ2.4 to ꢀ7.5 kcal/mol).
In the case of the [5a][X] (X = Cl, Br, I) ion pairs, two
geometries were considered, cis and trans to the alkylated
nitrogen atom (Figure 5, iv and v). The results, summarized in
Table 4, indicate that in all three cases the trans structure is
preferred. This is consistent with the results of previous
calculations of the electrostatic potential maps of the borane
adducts of chalcogenadiazoles which showed that the most
prominent
nitrogen.12
σ hole on the chalcogen is opposite to the substituted
Table 6. Electron density and its Laplacian at the Bond Critical Points of the Se…X and
Se…N supramolecular interactions in 4[5a]2[I]2.
Table 4. Contributions to the energy of interaction (kJ/mol) between the halide anions
Se…N
Se…I
and 5a in cis and trans geometries of [5a][X] (X=Cl, Br, I) ion pairs.
AIM Parameter
at BCP
long
3.81
2.38
short
8.24
6.67
Partition
X
EInt
EElstat
EPauli
EOrb
EDisp
ρ (e/Å3 x 102)
3.69
4.67
Scheme
Cl
Br
I
ꢀ520.8
ꢀ492.8
ꢀ461.4
ꢀ543.1
ꢀ516.1
ꢀ487.5
ꢀ545.8
ꢀ512.0
ꢀ470.7
ꢀ558.9
ꢀ521.0
ꢀ475.8
284.0
263.2
232.7
375.5
345.1
310.8
ꢀ255.2
ꢀ239.6
ꢀ217.7
ꢀ357.2
ꢀ337.3
ꢀ319.1
ꢀ3.8
ꢀ4.4
ꢀ5.7
ꢀ2.5
ꢀ2.9
ꢀ3.4
∇2ρ (e/Å5 x 102)
iv
The Se…N interactions in
4[5a]2[I]2 were also examined
Cl
Br
I
through Bader’s theory of atoms in molecules (AIM).52
Previous studies12 applied AIM to the examination the Lewis
acidity and basicity of 1-3; their results highlighted the
ambiphilic character of the chalcogenadiazoles molecules and
showed that the attachment of a Lewis acid to one nitrogen of
the heterocycle strengthens the [EꢀN]2 supramolecular synthon
formed by the other nitrogen. The calculated electron density
v
The dimerization energies the [5a][X] ion pairs were evaluated
in two possible geometries (Figure 5, vi and vii), the results are
compiled in Table 5. While dimer vi is formed from the cis (iv)
structures and contains the [SeꢀN]2 supramolecular synthon, the
trans (v) models form the [Se X]2 supramolecular synthon in
dimer vii. The energy of interaction is more negative in latter
case, which indicates that the structure of the dimer of the
methyl cation experimentally observed in the crystal of [5a][I]
salt is favoured by the greater stability of the trans geometry of
the ion pair. The results also show that the dimerization of the
ion pairs [5a][I] is stronger than the interaction of the ion pair
(ρ(r)) and its Laplacian (
(BCPs) of 5a]2[I]2 are given in Table 6. Although the
∇
2ρ(r)) at the bond critical points
4[
difference of Se…N distances is small, the AIM parameters
suggest that they are very different in strength as there is
indication that the energy of interaction scales linearly with the
BCP density.
For comparison, the corresponding BCP parameters of the Se…I
interaction in the pseudoꢀtrimer are included in Table 6. It is
interesting that while the BCP electron density is smaller, the
its Laplacian is intermediate between the values for the Se…N
SBIs. The comparison was further extended by calculating the
BCP parameters of the dimers of [5a][X] (X=Cl, Br, I) in the
two possible conformations considered under partition schemes
vi and vii. The results are compiled in Table 7. All these values
suggest that the Se…X and Se…N interactions are of similar
strength. In some cases, the calculated BCP parameters
approach those of the Te…N SBI in the neutral dimer of 1,2,5ꢀ
telluradiazole (4.20 e/Å3x10ꢀ2 and 10.9 e/Å5x10ꢀ2)12.
with the neutral molecule of 4; however, the overall sum of
interactions favours the formation of the pseudoꢀtrimer.
Table 5. Calculated contributions to the binding energies for the dimers of the [5a][X]
(X=Cl, Br, I) ion pairs.
Partition
X
EInt
EElstat
EPauli
EOrb
EDisp
Scheme
Cl
Br
I
ꢀ61.2
ꢀ64.3
ꢀ63.7
ꢀ57.2
ꢀ65.4
ꢀ71.6
ꢀ60.5
ꢀ68.2
ꢀ75.2
ꢀ172.6
265.1
298.5
51.4
66.23
87.1
ꢀ39.6
ꢀ48.6
ꢀ12.3
ꢀ13.7
ꢀ14.7
ꢀ16.2
ꢀ17.8
ꢀ19.3
vi
ꢀ61.0
Cl
Br
I
242.3
ꢀ187.8
ꢀ206.8
ꢀ110.7
ꢀ124.8
ꢀ144.0
vii
The pseudoꢀtrimer structures
4[5a]2[X]2 (X = I, BF4) are
especially interesting because of their two distinct Se…N SBI
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Table 7. Electron density and its Laplacian at the Bond Critical Points of the Se…
X
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AIM Parameter at BCP
Structure
X
Cl
Br
I
ρ (e/Å3 x 102)
∇2ρ (e/Å5 x 102)
7.95
8
6.67
9
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1.11
2.91
5.73
5.93
via
10
1.82
2.51
4.79
4.13
1.19
2.37
Cl
Br
I
3.45
8.07
11
12
13
14
15
16
vii
3.71
8.41
3.91
8.67
a. Short (top) and long (bottom) Se…X interactions.
Conclusions
As these investigations show, the most convenient method for
the preparation of Nꢀalkyl benzoselenadiazolium cations is the
condensation of selenous acid with Nꢀsubstituted
phenylenediamines. Such intermediates can be conveniently
obtained from oꢀfluoronitrobenzene and primary amines. As a 17
wide variety of aromatic diamines are commercially available
or readily prepared, this approach will certainly enable the
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18
preparation of a diversity of polycations that will be useful as
building blocks for supramolecular structures, including species
capable of forming large supramolecular aggregates. However,
19
the Nꢀalkyl benzoselenadiazolium cations have a strong affinity
for halide anions, therefore the anions must be replaced for
nonꢀcoordinating ions in order to enable the selfꢀassembly of
the building blocks through Se…N supramolecular interactions.
In contrast to the telluradiazoles, and as a great advantage, the
cations are not only stable in air but also in neutral to acidic
aqueous media.
20
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Acknowledgements
25
26
27
28
29
30
31
32
33
34
35
36
The financial support of the Natural Science Engineering
Research Council of Canada (NSERC, DGꢀIVB, PGSDꢀLML)
and the Ontario Graduate Scholarship program (LML) is
gratefully acknowledged. Portions of this work were made
possible by the facilities of the Shared Hierarchical Academic
Research Computing Network (SHARCNET: www.sharcnet.
ca) and Compute/Calcul Canada.
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DOI: 10.1039/C5DT04314J
Synthetic, Structural, and Computational Investigations of N-alkyl Benzo-
2,1,3-Selenadiazolium Iodides and their Supramolecular Aggregates
Lucia M. Lee, Victoria B. Corless, Michael Tran, Hilary Jenkins, James F. Britten and Ignacio Vargas-Baca*
Graphical Abstract
Alkyl benzo-2,1,3-selenadiazolium cations are conveniently prepared by cyclo-condensation of
N-alkyl-phenylenediamines with selenous acid