Diiodoacetylene: Compact, strong ditopic halogen bond donor

Article abstract of DOI:10.1039/c2ce00029f

Diiodoacetylene, C₂I₂, is the smallest ditopic halogen bond donor other than I₂ or other dihalogens. A convenient synthesis of diiodoacetylene from the common Sonagashira coupling reagent Me₃SiC≡CH, is described. The halogen-bonded adducts of C ₂I₂ with dimethylformamide (DMF), pyrazine (pyz) and 1,4-diazabicyclooctane (dabco) have been characterised by X-ray crystallography. All adopt 1D halogen-bonded chains linked via short C-I...O [I...O 2.834(4)-2.888(4) A; C-I...O > 170°] or C-I...N [I...N 2.715(3)-2.832(7) A; C-I...N > 175°] interactions. Attempts to synthesise the adduct of C₂I₂ with hexamethylenetetramine (hmta) resulted in isolation and crystallographic characterisation of the adduct of C₂I₄·hmta, indicating decomposition of C₂I₂ to yield C ₂I₄ in solution. The adduct comprises two independent C₂I₄ molecules that act, respectively, as tetratopic and ditopic halogen bond donors forming C-I...N interactions [I...N 2.948(7)-2.999(8) A; C-I...N > 165°], occupying three of the four nitrogen sites on htma. The remaining nitrogen sites engage in N...C(π) interactions directed orthogonal to the plane of the ditopic C₂I₄ molecules. Separate surveys of halogen bonds formed by diiodo(poly)alkynes I(C≡C)_nI (n = 1-3) and by C ₂I₄ molecules indicate that C-I...N halogen bonds are shorter, when normalised for van der Waals radii, and, by inference, stronger than halogen bonds involving other acceptor groups, and demonstrates that C _sp-I...N halogen bonds are generally shorter Csp ²-I...N halogen bonds. The Royal Society of Chemistry 2012.

Full text of DOI:10.1039/c2ce00029f

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PAPER
Diiodoacetylene: compact, strong ditopic halogen bond donor†
*
Catherine Perkins,‡ Stefano Libri, Harry Adams and Lee Brammer
Received 8th January 2012, Accepted 10th February 2012
DOI: 10.1039/c2ce00029f
Diiodoacetylene, C2I2, is the smallest ditopic halogen bond donor other than I2 or other dihalogens. A
convenient synthesis of diiodoacetylene from the common Sonagashira coupling reagent
Me3SiChCH, is described. The halogen-bonded adducts of C2I2 with dimethylformamide (DMF),
pyrazine (pyz) and 1,4-diazabicyclooctane (dabco) have been characterised by X-ray crystallography.
ꢀ
All ꢀadopt 1D halogen-bonded chains linked via short C–I/O [I/O 2.834(4)–2.888(4) A; C–I/O >
ꢀ
ꢀ
170 ] or C–I/N [I/N 2.715(3)–2.832(7) A; C–I/N > 175 ] interactions. Attempts to synthesise the
adduct of C2I2 with hexamethylenetetramine (hmta) resulted in isolation and crystallographic
characterisation of the adduct of C2I4$hmta, indicating decomposition of C2I2 to yield C2I4 in solution.
The adduct comprises two independent C2I4 molecules that act, respectively, as tetratopic andꢀditopic
ꢀ
halogen bond donors forming C–I/N interactions [I/N 2.948(7)–2.999(8) A; C–I/N > 165 ],
occupying three of the four nitrogen sites on htma. The remaining nitrogen sites engage in N/C(p)
interactions directed orthogonal to the plane of the ditopic C2I4 molecules. Separate surveys of halogen
bonds formed by diiodo(poly)alkynes I(ChC)nI (n ¼ 1–3) and by C2I4 molecules indicate that C–I/N
halogen bonds are shorter, when normalised for van der Waals radii, and, by inference, stronger than
halogen bonds involving other acceptor groups, and demonstrates that Csp–I/N halogen bonds are
generally shorter Csp2–I/N halogen bonds.
which remain the strongest halogen bond donors quantified
to date.
Diiodoacetylene can be viewed as one of a family of the
Introduction
Haloalkynes have a well-established role in synthetic organic
chemistry,1 but their application in supramolecular chemistry is
less well developed despite a long history. Haloalkynes can form
halogen bonds,2 in this context involving the attractive inter-
action of a C–I group with a Lewis base. More generally, the
study of halogen bonds has expanded dramatically over the past
10 years,3 resulting in applications in areas such as conducting
materials,4 liquid crystals,5 anion recognition6 and even struc-
tural biology.7 Halogen-bonded adducts of 1-iodoalkynes with
Lewis bases were first reported many decades ago,8 but the
ability of iodoalkynes to act as halogen bond donors in solution
was clearly established by Laurence and coworkers some 30
years ago using IR spectroscopy.9 Their study further showed
that the change in stretching frequency DnC–I upon halogen-
bonded adduct formation can be correlated to the halogen bond
enthalpy. Thus, iodoalkynes form strong halogen bonds with
a variety of Lewis bases, although are not as strong halogen
bond donors as ICN, I2 and the interhalogens IBr and ICl,
simplest linear ditopic halogen bond donors I–(ChC)n–I,
members of which are known for 0 # n # 4,10 and for which
halogen-bonded adducts have been characterised for n # 3. A
large number of halogen-bonded adducts and networks are
known for I2 (n ¼ 0), including halogen bonds to nitrogen
heterocycles11 and as part of polyiodide anions and networks.12
Very few studies of halogen bonding have been undertaken for
the longer diiodopolyalkynes (n $ 2). Indeed all have been
reported by Goroff and coworkers, who have described adducts
of I–(ChC)2–I (8 structures), I–(ChC)3–I (3 structures).10,13
Diiodo-acetylene itself has been crystallographically charac-
terised and forms a network of T-shaped C–I/p halogen
bonds14 in an analogous manner to the C–H/p hydrogen-
bonded network in acetylene.15 Halogen-bonded adducts of
diiodoacetylene have been reported (13 structures) with oxygen
bases,16 a sulphur base,17 a selenium base17 and most commonly
with halide ions.18 Here we report a convenient synthesis of
diiodoacetylene and its halogen-bond adducts with nitrogen and
oxygen bases (pyrazine, dabco and DMF). We further report
its ease of decomposition to yield tetraiodoethylene and the
subsequent formation of the C2I4$hmta (4) adduct from one such
decomposition. Halogen bond donors and acceptors are shown
in Scheme 1.
Department of Chemistry, University of Sheffield, Brook Hill, Sheffield S3
7HF, UK. E-mail: lee.brammer@sheffield.ac.uk
† Electronic supplementary information (ESI) available. CCDC
reference numbers 865218–865221. For ESI and crystallographic data
in CIF or other electronic format see DOI: 10.1039/c2ce00029f
‡ Current address: Department of Chemistry, University of Liverpool,
Crown Street, Liverpool L69 7ZD, UK.
This journal is ª The Royal Society of Chemistry 2012
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crystals of 1 suitable for single crystal X-ray diffraction were
obtained after 3 days (4.2 mg, 0.012 mmol, 65.2% yield). Calcd: C
20.13%, H 1.13%, N 7.83%, I 70.91%. Found: C 20.17%, H
0.92%, N 7.73%, I 67.68%.
C2I2$dabco (2). C2I2 (5 mg, 0.018 mmol) was dissolved in
CH2Cl2 (ca. 2 mL) and dabco (2.2 mg, 0.018 mmol) was dissolved
in EtOH (ca. 2 mL). The latter solution was layered on the
former with a buffer layer of CH2Cl2 (ca. 1 mL). Large yellow
block crystals of 2 suitable for single crystal X-ray diffraction
were obtained after 3 days (6.0 mg, 0.0154 mmol, 85.5% yield).
C2I2$DMF (3). C2I2 (5 mg, 0.018 mmol) was dissolved in
CH2Cl2 (ca. 1 mL). Slow evaporation over 3 days yielded yellow
block crystals that were suitable for single crystal X-ray
diffraction of the C2I2$DMF adduct (3), indicating that DMF
had not been fully removed from the previously synthesised C2I2.
C2I4$hmta (4). C2I2 (5 mg, 0.018 mmol) was dissolved in
CH2Cl2 (ca. 2 mL) and hexamethylenetetramine (hmta) (1.2 mg,
0.009 mmol) was dissolved in EtOH (ca. 2 mL). The latter
solution was layered on the former with a buffer layer of CH2Cl2
(ca. 1 mL). Small yellow plate crystals of 4 suitable for single
crystal X-ray diffraction were obtained after 3 days. The product
was not phase pure.
Scheme 1 Halogen bond donors (left) and acceptors (right) used in
adduct formation.
X-ray crystallography
X-Ray data for compounds 1–4 were collected on a Bruker APEX
II diffractometer using graphite-monochromated Mo-Ka radia-
tion. Low temperature data collections were undertaken using
either an Oxford Cryosystems Cobra or N-HeliX low temperature
device. Intensity data wereindexed and integrated using the APEX
II suite of programs.20 Details of the crystal, data collection and
refinement parameters are summarized in Table 1. Data were
corrected for absorption using empirical methods (SADABS)
based upon symmetry-equivalent reflections combined with
measurements at different azimuthal angles.21 The structures were
solved by direct methods and refined by full-matrix least squares
onweightedF 2 valuesforallreflectionsusingeithertheSHELXTL
program22 or SHELXL via the OLEX-2 suite of crystallographic
programs.23 Non-hydrogen atoms were refined anisotropically.
Hydrogen atoms were placed in calculated positions, refined using
idealized geometries (riding model), and assigned fixed isotropic
displacement parameters. In the crystal structure of 1, both
moleculesaresituatedatcentresofinversion, whereasinthe crystal
structure of 2 both molecules are situated on mirror planes. The
crystal structure of 4 exhibits rotational disorder about two sepa-
rate axes for one of the two independent C2I4 molecules (see ESI†
for more details). The crystal structure of 4 has been reported
previously at 296 K.24 Although the unit cell reported is very
similar to that observed in our 120 K study, the space group C2/m
was used rather than P21/c in the present study. Rotational
disorder of the C2I4 molecule was reported about only one axis.
Experimental
General
All reagents were purchased from Fluorochem Ltd., Alfa Aesar
or Lancaster Synthesis Inc. and used as received.
Synthesis
1,2-diiodoacetylene, C2I2. N-iodosuccinamide (NIS) (1.395 g,
6 mmol) and AgNO3 (0.086 g, 0.5 mmol) were dried under
vacuum for 10 mins. Trimethylsilylacetylene (TMSA) (0.5 mL,
5.1 mmol) followed by DMF (10 mL) was added to a mixture of
the two reactants and allowed to stir for 30 mins. After this time
GC-MS analysis showed the presence of 1,2-diiodoacetylene
(5.29 mins) and 1-iodo-2-(trimethylsilyl)acetylene (4.35 mins),
indicating that the monoiodo(silyl)alkyne intermediate could not
be isolated by this method. After a further 30 mins of reaction
only 1,2-diiodoacetylene was present (i.e. 100% conversion by
GC-MS). The reaction mixture was then filtered, the product
extracted with diethyl ether, dried with MgSO4 and the solvent
removed in vacuo. Although C2I2 can be handled as solid, it has
been shownꢀto decompose explosively at temperatures between
80 and 130 C or due to shock.19 Thus, the compound was not
isolated and was stored in CH2Cl2 solution as a precaution.
Crystal syntheses
C2I2$pyz (1). C2I2 (5 mg, 0.018 mmol) was dissolved in CH2Cl2
(ca. 2 mL) and pyrazine (1.4 mg, 0.018 mmol) was dissolved in
EtOH (ca. 2 mL). The latter solution was layered on the former
with a buffer layer of CH2Cl2 (ca. 1 mL). Large yellow block
Results
The synthesis of diiodoacetylene was first reported in 1865,
involving the reaction of silver acetylide with iodine in ether.25
A
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Table 1 Data collection, structure solution and refinement parameters for 1–4
C2I2$pyz (1)
C2I2$dabco (2)
C2I2$DMF (3)
C2I4$hmta (4)
Crystal colour
Crystal size/mm
Crystal system
Space group, Z
yellow
0.02 ꢁ 0.05 ꢁ 0.29
yellow
yellow
yellow
0.03 ꢁ 0.021 ꢁ 0.012
Monoclinic
P21/m, 2
6.5418(2)
8.2834(3)
10.3370(3)
90.00
101.233(2)
90.00
549.41(3)
2.357
120
5.678
3.18 to 27.49
4640
1345 (0.0236)
1345
67
0
0.0268
0.0433
1.033
0.015 ꢁ 0.01 ꢁ 0.008
Monoclinic
P21/n, 4
5.575(3)
14.420(7)
11.901(6)
90.00
103.109(8)
90.00
931.8(8)
2.501
120
6.686
3.33 to 25.68
5749
1726 (0.0369)
1726
84
0
0.0304
0.0864
1.031
0.43 ꢁ 0.28 ꢁ 0.19
Monoclinic
P21/c, 4
15.9274(7)
11.0145(4)
8.7574(4)
90.00
92.800(2)
90.00
1534.5(1)
2.908
120
8.106
2.25 to 27.52
15 754
3358 (0.0356)
3358
176
51
0.0491
0.0952
1.208
Triclinic
ꢁ
P1, 1
ꢀ
a/A
4.2383(6)
7.3655(10)
7.8486(10)
113.047(4)
99.614(4)
93.365(4)
220.20(5)
2.699
293
7.071
2.88 to 27.49
3429
1004 (0.0216)
1004
46
0
0.0401
ꢀ
b/A
ꢀ
c/A
a (ꢀ)
b (ꢀ)
g (ꢀ)
3
ꢀ
V/A
Density/Mg mꢂ3
T/K
m/mmꢂ1
q range/ꢀ
Reflections collected
Independent reflections (Rint
)
Reflections used in refinement, n
L.S. parameters, p
Restraints, r
R1(F),a I > 2.0s(I)
wR2(F2),a all data
S(F2),a all data
0.1307
1.234
a
2
2
4
2
2
R1(F) ¼ S(|Fo| ꢂ |Fc|)/S|Fo|; wR2(F2) ¼ [Sw(Fo ꢂ Fc )2/SwFo
]
1/2; S(F2) ¼ [Sw(Fo ꢂ Fc )2/(n + r ꢂ p)]1/2
.
number of other syntheses have since been reported.19,26 Here we
report a convenient synthesis from the reagent trimethylsilyla-
cetylene (TMSA), commonly deployed when linking two arenes
via an alkyne bridge using two consecutive Sonogashira coupling
reactions.27 Iodination of TMSA using N-iodosuccinamide and
AgNO3 yields diiodoacetylene as the sole product after 1 h,
consistent with contemporary methods for direct halogenation of
protected alkynes.10,28 Adducts C2I2$pyz (1) and C2I2$dabco (2)
were prepared by layering solutions of the two components,
whereas crystals of C2I2$DMF (3) were obtained upon recrys-
tallisation of diiodoacetylene from CH2Cl2, adduct formation
arsing from a small amount of residual DMF remaining from the
original synthesis of diiodoacetylene. Attempts to prepare
adducts of C2I2 with hexamethylenetetramine (hmta) resulted in
decomposition of C2I2 to liberate iodine resulting in conversion
of residual C2I2 to tetraiodoethylene, C2I4.29 In our study we
were able to isolate the adduct C2I4$hmta (4).
lone pair directions (C]O/I 125.1(4), 145.4(4)ꢀ; I/O/I
89.4(1)ꢀ) presumably to accommodate other intermolecular
interactions (notably C–H/p).
The crystal structure of C2I4$hmta (4) is shown in Fig. 3. Two
independent C2I4 molecules, each of which has crystallographic
inversion symmetry, link htma molecules via a C–I/N halogen-
bonded network of corrugated sheets (Fig. 3a) that involves
three of the four nitrogen atoms on each htma molecule
ꢀ
(I/N 2.948(7), 2.997(8), 2.999(8) A; C–I/N 166.6(3), 169.2(3),
170.9(3)ꢀ). The fourth nitrogen atom interacts orthogonal to
the C2I4 plane with the molecule that participates in only two
C–I/N halogen bonds (Fig. 3b). The nitrogen lone pair is
directed approximately at one of the two alkene carbon atoms
The crystal structures of adducts 1 and 2 are shown in Fig. 1.
Combination of linear ditopic halogen bond donor (C2I2) and
acceptor in both cases results in a parallel linear assemblies
ꢀ
propagated by C–I/N halogen bonds (I/N 2.832(7) A; C–I/
N 175.3(3)ꢀ in 1; I/N 2.715(3), 2.719(4) A; C–I/N 178.2(2),
ꢀ
178.7(2)ꢀ in 2). Interactions between neighbouring halogen-
bonded chains include C–H/p hydrogen bonds between pyr-
azine or dabco and the p-bond of the alkynes. The crystal
structure of 3 comprises zigzag chains in which the carbonyl
oxygen acts as a bifurcated halogen bond acceptor (Fig. 2; I/O
ꢀ
ꢀ
2.834(4), 2.888(4) A; C–I/O 170.7(2), 173.0(2) ) in a manner
analogous to the well-established behaviour of carbonyl groups
as hydrogen bond acceptors.30 Parallel chains are linked via
C–H/p hydrogen bonds involving the methyl hydrogen atoms
of the DMF molecules to give a sheet; the sheets then stack in an
antiparallel manner. The halogen bond geometry at the acceptor
oxygen atom deviates from the 120ꢀ angles anticipated from the
Fig. 1 Linear halogen-bonded assemblies of (a) C2I2$pyz (1) and
(b) C2I2$dabco (2). C–I/N halogen bonds are shown as dashed lines.
C–H/p hydrogen bonds between chains are not shown.
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ESI†). The two remaining iodine atoms, which do not participate
in C–I/N halogen bonds, form C–I/I–C interactions with
neighbouring molecules.
Discussion
Crystal structures of 2, 3 and 4 show that diiodoacetylene forms
short linear halogen bonds to both nitrogen and oxygen acceptor
groups with normalised bond distances31 as short as RIN 0.80 (1),
RIN 0.77 (2) and RIO 0.81 (3). These are among the shortest
halogen bonds recorded for diiodo(poly)alkynes I(ChC)nI
(n ¼ 1–3) which collectively form short halogen bonds across
a variety of acceptor groups (Fig. 4). Mosthalogen bonds are close
to linear in geometry (C–I/X $ 170ꢀ), with only a few excep-
tions.32 There is no discernable difference between halogen bond
geometries for the different polyalkynes. However, it is noticeable
that halogen bonds to nitrogen are generally shorter and by
inference stronger than those formed by other acceptor groups,
the majority having RIN # 0.80. A qualitative ranking of halogen
bond lengths based upon the data currently available for these
diiodo(poly)alkynes isRIN <RIO <RICl <RIBr <RII # RIS z RISe
.
Fig. 2 Zigzag halogen-bonded assemblies of C2I2$DMF. C–I/O
halogen bonds are shown as dashed lines. C–H/p hydrogen bonds
between chains are not shown.
Decomposition of iodoalkynes to liberate iodine is well docu-
mented. Indeed the original impetus for the extensive work by
Goroff and coworkers on diiodopolyalkynes was their ease of
degradation to Cn species that might be used in construction of
smaller all-carbon molecules than the most well known fullerenes
(C60, C70, etc).10 The degradation of diiodoacetylene to yield tet-
raiodoethylene has also previously been observed by Yamamoto,
who reported a structure containing both C2I2 and C2I4 which
resulted from such degradation.18c In our case the only iodine-
containing product isolated and crystallographically charac-
terised was the C2I4$htma adduct (4). Intheir original reportof the
structure of C2I4$htma, Pennington, Hanks and coworkers note
that it is unusual to observe a C2I4 molecule that forms 4 C–I/N
halogen bonds.24 Indeed in 1 : 1 adducts with ditopic halogen
bond acceptors such a 4,4-bipyridine and similar species the C2I4
acts as linear connector via two C–I/N halogen bonds involving
trans iodine substituents. The two remaining iodine substituents
usually form C–I/I–C interactions with neighbouring molecules.
This is the case for the rotationally disordered C2I4 molecule in 4.
In a survey of 27 halogen-bonded C2I4 adducts identified in the
CSD (Nov 2010, version 1.13), ten structures form two C–I/N
halogen bonds and C–I/I–C interactions involving remaining
iodines. Two further structures adopt similar patterns but with
C–I/O or C–I/S halogen bonds instead of C–I/N. Eleven
structures form halogen bonds with all four C–I groups, seven of
these involving halide ions as the acceptor group. The remaining
four structures form either three halogen bonds or adopt a pattern
analogous to 4 in which one C2I4 molecule forms four halogen
bonds and a second independent molecule forms only two. Full
details are provided in Table S1, ESI.†
Fig. 3 Halogen-bonded assembly of C2I4$htma. (a) Showing corrugated
layer structure propagated via C–I/N halogen bonds and (b) showing
tetrahedral supramolecular coordination of htma via three C–I/N
halogen bonds and an N/C(p) interaction. Hydrogen atoms are omitted
for clarity. The C2I4 molecule that forms only two C–I/N halogen bonds
is disordered (Fig. S1, ESI†).
The geometries of the halogen bonds formed in adducts of
C2I4 are presented in Fig. 5. Type I C–I/I–C interactions are not
included, but type II contacts (i.e. C–I/I(C) halogen bonds) are
considered. Again it is clear that nitrogen atoms, principally in
neutral heterocyclic molecules provide excellent halogen bond
acceptor sites and often lead to short C–I/N interactions.
However, discrimination between other types of acceptor groups
is not apparent from the data. Halogen bonds involving C2I4 are
ꢀ
ꢀ
(N/C 3.367(9) A; N/C]C 89.2(5) ). One C2I4 molecule forms
four C–I/N halogen bonds, while the other forms two. The
latter alkene is both rotationally disordered about the normal to
its molecular plane and rotationally disordered about the I/I
vector involving the two halogen-bonded iodine atoms (Fig. S1,
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Fig. 4 Plot of normalised halogen bond length31
R
IX vs. C–I/X halogen bond angle (ꢀ) for ditopic halogen bond donors I(ChC)nI (n ¼ 1–3). Halogen
bond acceptor atoms (X) are distinguished by different coloured dots.
Fig. 5 Plot of normalised halogen bond length31
R
IX vs. C–I/X halogen bond angle (ꢀ) for tetratopic halogen bond donors I2C]CI2. Halogen bond
acceptor atoms (X) are distinguished by different coloured dots.
generally longer and, although mostly adopting geometries with
C–I/X $ 160ꢀ, deviate further from linear geometries than
those involving C2I2 (Fig. 4). This is consistent with the more
electron-withdrawing nature of sp hybridised carbon atoms over
sp2 hybridised carbon which results the relative halogen bond
strengths being Csp–I/X > Csp2–I/X (X ¼ acceptor group).
This behaviour parallels that of Csp–H/X and Csp2–H/X
hydrogen bonds.33 With respect to the two molecules being
studied, lengthening of the halogen bonds involving C2I4 may
also result from as a compromise in the need to accommodate
interactions with so many C–I groups in close proximity.
References
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Conclusions
A facile synthesis and of diiodoacetylene and crystal structures of
three new adducts with short C–I/N or C–I/O halogen bonds
are reported. The degradation of C2I2 to liberate iodine and
thereby generate tetraiodoethylene C2I4 is also documented, and
has resulted in isolation of the adduct C2I4$htma. The crystal
structure of this known adduct has been redetermined in
a different space group. Comparison of halogen bond geometries
of C2I2 with those of C2I4 across all reported crystal structures
indicates that the Csp–I group of the former results in shorter
halogen bonds that are closer to linear geometry than those of
the Csp2–I group of the latter.
ꢂ
Acknowledgements
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Sheffield for funding of this work.
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