Structure Direction, Solvent Effects, and Anion Influences in Halogen-Bonded Adducts of 2,6-Bis(iodoethynyl)pyridine

Article abstract of DOI:10.1021/acs.cgd.6b00766

A new divergent and self-complementary halogen bond donor-acceptor molecule 2,6-bis(iodoethynyl)pyridine L has been prepared and structurally characterized, and used to generate a series of extended halogen-bonded adducts with tetrabutylammonium halide salts. The reaction between L and anions such as either bromide or chloride gives the one-dimensional polymeric species {L·TBABr} or {L·TBACl}, respectively, which contains helical strands linked by C-I···X^- halogen bonds which partially encapsulate the associated organic cations. Varying the reaction solvent from ethyl acetate to 5:95 methanol/ethyl acetate gives rise to another polymeric phase on combining L with tetrabutylammonium chloride, the one-dimensional looped chain structure {L₂·TBACl} in which each chloride ion acts as a four-connected square planar node for halogen bonding interactions originating from L. Similar solvent effects are observed in the discrete macrocyclic species {L·TBAI}-α and {L·TBAI}-β, both consisting of cyclic (L₂I₂)^2- species which vary in their extended structures to adopt different packing modes, resembling those observed in the chloride and bromide adducts. Reaction of L with tetrabutylammonium fluoride in the presence of methanol gives a one-dimensional polymeric assembly {L₂·TBAF·MeOH} containing a unique MeOH···F^- node in which the strongly hydrogen-bonded anionic species is supported solely by four halogen bonding interactions. Excluding hydrogen bond donors from the reaction mixture affords {L₃TBAF₂}, an overall two-dimensional polymeric assembly consisting of a mixture of one- and two-dimensional networks based on iodine-fluoride halogen bonds. In all cases, the strong interactions between the iodoethynyl groups and halide anions overcome the tendency for L to form the self-complementary halogen-bonded network, showing that synthetically accessible heterocyclic iodoethynyl compounds present exciting new directions in the structural chemistry field.

Full text of DOI:10.1021/acs.cgd.6b00766

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Article
Structure direction, solvent effects and anion influences
in halogen-bonded adducts of 2,6-bis(iodoethynyl)pyridine
Dawn E. Barry, Chris S Hawes, Salvador Blasco, and Thorfinnur Gunnlaugsson
Cryst. Growth Des., Just Accepted Manuscript • DOI: 10.1021/acs.cgd.6b00766 • Publication Date (Web): 13 Jul 2016
Downloaded from http://pubs.acs.org on July 15, 2016
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Structure direction, solvent effects and anion influences in halogenꢀbonded
adducts of 2,6ꢀbis(iodoethynyl)pyridine
Dawn E. Barry, Chris S. Hawes,* Salvador Blasco & Thorfinnur Gunnlaugsson*
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School of Chemistry & Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin 2, Ireland.
Email: gunnlaut@tcd.ie
A
new divergent and selfꢀcomplementary halogen bond donorꢀacceptor molecule 2,6ꢀ
bis(iodoethynyl)pyridine L has been prepared and structurally characterized, and used to generate a series
of extended halogenꢀbonded adducts with tetrabutylammonium halide salts. The reaction between L and
either tetrabutylammonium bromide or chloride gives the oneꢀdimensional polymeric species {L·TBABr}
ꢀ
or {L·TBACl}, respectively, which contain helical strands linked by CꢀI···X halogen bonds which
partially encapsulate the associated organic cations. Varying the reaction solvent from ethyl acetate to
:95 methanol:ethyl acetate gives rise to another polymeric phase on combining L with
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tetrabutylammonium chloride, the oneꢀdimensional looped chain structure {L ·TBACl} in which each
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chloride ion acts as a fourꢀconnected square planar node for halogen bonding interactions originating
from L. Similar solvent effects are observed in the discrete macrocyclic species {L·TBAI}ꢀα and
2
ꢀ
{
L·TBAI}ꢀβ, both consisting of cyclic (L I ) species which vary in their extended structures to adopt
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different packing modes, resembling those observed in the chloride and bromide adducts. Reaction of L
with tetrabutylammonium fluoride in the presence of methanol gives a oneꢀdimensional polymeric
ꢀ
assembly {L ·TBAF·MeOH} containing a unique MeOH···F node in which the strongly hydrogenꢀ
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bonded anionic species is supported solely by four halogen bonding interactions. Excluding hydrogen
bond donors from the reaction mixture affords {L TBAF }, an overall twoꢀdimensional polymeric
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2
assembly consisting of a mixture of oneꢀ and twoꢀdimensional networks based on iodineꢀfluoride halogen
bonds. In all cases, the strong interactions between the iodoethynyl groups and halide anions overcome
the tendency for L to form the selfꢀcomplementary halogenꢀbonded network, showing that synthetically
accessible heterocyclic iodoethynyl compounds present exciting new directions in the structural chemistry
field.
Contact Author: Prof. Thorfinnur Gunnlaugsson
School of Chemistry and Trinity Biomedical Sciences Institute (TBSI)
Trinity College Dublin
Dublin 2, Ireland
Phone: +353ꢀ1ꢀ896 3459
Emails: hawescs@tcd.ie and gunnlaut@tcd.ie
https://thorrigunnlaugsson.wordpress.com/
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Structure direction, solvent effects and anion
influences in halogenꢀbonded adducts of 2,6ꢀ
bis(iodoethynyl)pyridine
Dawn E. Barry, Chris S. Hawes,* Salvador Blasco & Thorfinnur Gunnlaugsson*
School of Chemistry and Trinity Biomedical Sciences Institute (TBSI), Trinity College Dublin,
The University of Dublin, Dublin 2, Ireland. Email: gunnlaut@tcd.ie
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Abstract
A new divergent and selfꢀcomplementary halogen bond donorꢀacceptor molecule 2,6ꢀ
bis(iodoethynyl)pyridine L has been prepared and structurally characterized, and used to
generate a series of extended halogenꢀbonded adducts with tetrabutylammonium halide salts. The
reaction between L and anions such as either bromide or chloride gives the oneꢀdimensional
polymeric species {L·TBABr} or {L·TBACl}, respectively, which contain helical strands linked
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ꢀ
by CꢀI···X halogen bonds which partially encapsulate the associated organic cations. Varying
the reaction solvent from ethyl acetate to 5:95 methanol:ethyl acetate gives rise to another
polymeric phase on combining L with tetrabutylammonium chloride, the oneꢀdimensional
looped chain structure {L ·TBACl} in which each chloride ion acts as a fourꢀconnected square
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planar node for halogen bonding interactions originating from L. Similar solvent effects are
observed in the discrete macrocyclic species {L·TBAI}ꢀα and {L·TBAI}ꢀβ, both consisting of
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ꢀ
cyclic (L I ) species which vary in their extended structures to adopt different packing modes,
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resembling those observed in the chloride and bromide adducts. Reaction of L with
tetrabutylammonium fluoride in the presence of methanol gives a oneꢀdimensional polymeric
ꢀ
assembly {L ·TBAF·MeOH} containing a unique MeOH···F node in which the strongly
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hydrogenꢀbonded anionic species is supported solely by four halogen bonding interactions.
Excluding hydrogen bond donors from the reaction mixture affords {L TBAF }, an overall twoꢀ
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2
dimensional polymeric assembly consisting of a mixture of oneꢀ and twoꢀdimensional networks
based on iodineꢀfluoride halogen bonds. In all cases, the strong interactions between the
iodoethynyl groups and halide anions overcome the tendency for L to form the selfꢀ
complementary halogenꢀbonded network, showing that synthetically accessible heterocyclic
iodoethynyl compounds present exciting new directions in the structural chemistry field.
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Introduction
The directed and reversible assembly of multiꢀcomponent architectures has long been an area of
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significant interest in coordination and materials chemistry. Many supramolecular structures
and assemblies have been designed and constructed based on robust, directional and reversible
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interactions, principal among them the coordination bond and the hydrogen bond. More
recently, more subtle intermolecular interactions have been employed as reliable synthons in the
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construction of supramolecular assemblies, such as πꢀπ interactions and halogen bonding. The
latter phenomenon has attracted intense interest in recent years, and is sometimes considered as
an analogue to hydrogen bonding in strength, although with a much greater degree of
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directionality.
Since the phenomenon was first identified and methodically harnessed, many
elegant examples have emerged of the use of halogen bonding interactions in the formation of
multiꢀcomponent organic or metalꢀorganic assemblies, in the gaseous and solution states as well
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as in the solid state.
Now that substantial progress has been made towards adoption of the
halogen bond as an accessible supramolecular synthon, many new examples of halogen bond
donors are continually being discovered, alongside new applications for these materials in
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materials science.
In particular, halogen bonding constitutes an important aspect to
pharmaceutical polymorph screening, where the presence of such interactions can play an
important role in the nature and quantity of potential polymorphs of electron deficient
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haloarenes.
To date, much of the research into halogenꢀbonded adducts has focused on iodoꢀ
perfluoroaryl compounds such as 1,4ꢀdiiodoꢀ2,3,5,6ꢀtetrafluorobenzene and related isomers, and
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iodoperfluoroalkanes.
These compounds make for attractive starting materials based on their
ready availability and good stability, and possess the requisite σꢀhole electronic nature to allow
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for robust interactions with various Lewisꢀbasic groups. Other electron withdrawing substituents
such as nitro and trifluoromethyl are also becoming increasingly widespread, to increase the
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Lewis acidity of iodine groups leading to stronger halogen bonding interactions.
Other
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molecular platforms for halogen bonding are somewhat less common, but include the notably
reactive halogenated dialkynes 1,4ꢀdiiododiacetylene and 1,4ꢀdibromodiacetylene. Both
compounds have been stabilized in the solid state through strong halogen bonding interactions
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with pyridine donors, allowing for their controlled topochemical polymerization.
Although
unsubstituted bisꢀhaloalkynes are challenging to handle due to their tendencies towards violent
polymerization, alkyneꢀ and haloalkyneꢀsubstituted aromatics and heterocycles are
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comparatively stable and are used as precursors in a wide variety of organic transformations.
In several reports, Resnati, Aakeröy and others have used phenyl iodoalkynes to great effect in
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the formation of halogen bonded adducts with various Lewis bases.
Herein we report the
synthesis and structural chemistry of a new bis(iodoalkyne)ꢀsubstituted pyridine species 2,6ꢀ
bis(iodoethynyl)pyridine L, which represents an unusual example of a molecule containing both
strong halogen bond donor and acceptor sites, and probe its behavior as a ditopic halogen bond
donor in the presence of halide anions.
Experimental
Materials & Methods
All reagents, solvents and starting materials were purchased from SigmaꢀAldrich, Merck or
Fisher Scientific, were of reagent grade or better, and were used as received. 2,6ꢀ
Diethynylpyridine was prepared according to literature procedures, and characterization data
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were consistent with that previously reported. ESI mass spectra were acquired using a
Micromass time of flight mass spectrometer (tof), interfaced to a Waters 2690 HPLC. The
instrument was operated in positive or negative mode as required. Leucine Enkephalin was used
as an internal lock mass. Masses were recorded over the range 100ꢀ1000 m/z. Operating
conditions were as follows: ESI capillary voltage 2500V, cone voltage 25V, desolvation
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temperature 300 C, source temperature 100 C. The ESI gas was nitrogen. MassLynx 4.0
software was used to carry out the analysis. Elemental analyses were carried out at the
Microanalytical Laboratory, School of Chemistry and Chemical Biology, University College
Dublin. NMR data were recorded in commercially available deuterated solvents on a Bruker
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Spectrospin DPXꢀ400 spectrometer which operates at 400.13 MHz for H NMR and 100.6 MHz
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for C NMR. Tetramethylsilane (TMS) was used as an internal standard and shifts were
referenced relative to the internal solvent signals with chemical shifts expressed in parts per
million (ppm / δ). Infrared spectra were recorded on a Perkin Elmer Spectrum 100 FTIR
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spectrometer with universal ATR sampling accessory, in the range 4000 – 550 cm . Xꢀray
powder diffraction patterns were collected using a Bruker D2 Phaser instrument with Cu Kα
radiation (λ = 1.5418 Å). Samples were ground and mounted on silicon sample holders, and data
were collected in the 2θ range 5 – 55° at room temperature while rotating φ at a speed of 1 RPM.
Sample background due to fluorescence was subtracted and the patterns were compared with
those simulated from the single crystal data collected at 100 K.
Synthesis of 2,6ꢀbis(iodoethynyl)pyridine L
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The title compound was prepared by a modification to a reported procedure for the synthesis of
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the monoꢀsubstituted equivalent 2ꢀiodoethynylpyridine. To a solution of 2,6ꢀdiethynylpyridine
0.9 g, 6.8 mmol) and potassium iodide (2.5 g, 15 mmol, 2.2 equiv.) in CH OH (60 mL) a
(
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solution of 70% aqueous tertꢀbutyl hydroperoxide (2.84 mL, 20.4 mmol, 3 equiv.) was added
dropꢀwise over a period of 30 mins with stirring at RT. The reaction mixture was stirred at RT
for a further 24 hrs and was then quenched with sat. aq. Na S O , washed with brine and the
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product extracted into ethyl acetate. The organic layer was dried over MgSO and solvent
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removed in vacuo, affording the pure product as a brown microcrystalline solid. Yield 1.467 g
(57%). Single crystals suitable for Xꢀray diffraction were prepared by recrystallization from
ethyl acetate, and Xꢀray powder diffraction confirmed that the original microcrystalline material
matches this phase. m.p. 189ꢀ196 °C (decomp.); Found C, 28.66; H, 0.67; N, 3.50; Calculated for
1
C H NI C, 28.53; H, 0.80; N, 3.70%; H NMR (400 MHz, CDCl ) δ 7.62 (1H, t, J = 7.8 Hz,
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H:
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pyridineꢀH), 7.34 (2H, d, J = 7.8 Hz, pyridineꢀH); C NMR (100 MHz , CDCl ) δ 143.23,
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C:
+
+
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36.51, 127.07, 93.33, 60.40; HRMS (m/z) (ESI ) Calculated for C H NI m/z = 379.8433 [M +
9 4 2
+
ꢀ1
H] . Found m/z = 379.8429; νmax (ATR, cm ) 3057w, 2959m sh, 2871w, 2153m, 1574s, 1552s,
1436s, 1381w, 1242m, 1210w, 1155w, 1079w, 992w, 984w, 953w, 800s, 749w, 733m, 609m.
Phase purity was confirmed by Xꢀray powder diffraction (Supporting Information).
Synthesis of halogenꢀbonded adducts
Synthesis of {LꢁTBABr}
A solution of L (20 mg, 53 ꢁmol) was prepared in 2 mL of ethyl acetate with the aid of
sonication and gentle heating. This solution was added to a solution of tetrabutylammonium
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bromide (17 mg, 53 ꢁmol) in ethyl acetate (2 mL). A white suspension formed immediately on
mixing. The mixture was sealed and left to stand for 24 hours, at which time the colourless
crystals were isolated by filtration, washed with ethyl acetate, and dried in air. Yield 12 mg (30
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%
). m.p. 155ꢀ157 °C (decomp); Found C, 42.39; H, 5.50; N, 3.86; Calculated for C H N BrI
25 39 2 2
ꢀ1
C, 42.82; H, 5.61; N, 3.99%; νmax (ATR, cm ) 3055w, 2961m sh, 2872m, 2158m, 1563s, 1553s,
1
480m sh, 1460m, 1431s, 1380m, 1343w, 1297w, 1268m, 1238m, 1206m, 1149m, 1079m,
028w, 1003w, 980m, 947m, 877m sh, 824s, 742s. Phase purity was confirmed by Xꢀray powder
1
diffraction (Supporting Information).
Synthesis of {LꢁTBACl}
The title compound was prepared through an identical procedure to {L·TBABr}, using 15 mg
(54 ꢁmol) of tetrabutylammonium chloride. Yield 6 mg (17 %). m.p. 151ꢀ154 °C (decomp);
Found C, 45.71; H, 6.02; N, 4.12; Calculated for C H N ClI C, 45.71; H, 5.98; N, 4.26%; ν
max
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39
2
2
ꢀ1
(
ATR, cm ) 3058w, 2962m sh, 2872m, 2157m, 1563s, 1551s, 1479m sh, 1463m, 1430s, 1380m,
1
342w, 1300w, 1269m, 1236m, 1205s, 1149s, 1079m, 1030w, 1004w, 980m, 946m, 878m sh,
25s, 742s. Phase purity was confirmed by Xꢀray powder diffraction (Supporting Information).
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Synthesis of {L ꢁTBACl}
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A solution of L (20 mg, 53 ꢁmol) in 2 mL of 5:95 methanol:ethyl acetate was added to a solution
of tetrabutylammonium chloride (8 mg, 29 ꢁmol) in 2 mL of 5:95 methanol:ethyl acetate. The
mixture was allowed to concentrate by slow evaporation, yielding colourless crystals after 12
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hours. The crystals were isolated by filtration, washed with ethyl acetate, and dried in air. Yield
21 mg (75 %). m.p. 139ꢀ142 °C (decomp); Found C, 39.35; H, 4.04; N, 3.90; Calculated for
ꢀ1
C H N ClI C, 39.43; H, 4.09; N, 4.06%; ν (ATR, cm ) 3057w, 2962m sh, 2873m, 2153m,
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max
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574s, 1553s, 1480m sh, 1437s, 1379w, 1281m, 1241m, 1210s, 1156m, 1079w, 1027w, 981m,
950m, 877m, 809s, 743m, 733m. Phase purity was confirmed by Xꢀray powder diffraction
Supporting Information).
(
Synthesis of {LꢁTBAI}ꢀα
A solution of L (20 mg, 53 ꢁmol) in 2 mL of ethyl acetate was prepared with brief sonication
and gentle heating. This mixture was added to a suspension of tetrabutylammonium iodide (20
mg, 54 ꢁmol) in ethyl acetate (5 mL), and the mixture was heated at reflux for 30 minutes. On
cooling to room temperature a white suspension formed, and the solution was left to stand
overnight, giving colourless crystals which were isolated by filtration, washed several times with
ethyl acetate, and dried in air. Yield 11 mg (28 %). m.p. 116ꢀ119 °C (decomp.); Found C, 40.00;
ꢀ1
H, 5.19; N, 3.63; Calculated for C H N I C, 40.13; H, 5.25; N, 3.74%; ν (ATR, cm )
max
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39 2 3
3
057w, 2958m sh, 2872m, 2153m, 1574s, 1551s, 1485m, 1467m sh, 1433s, 1378m, 1293w,
1267m, 1242m, 1205s, 1145m, 1108w, 1075m sh, 1031m, 982m, 945s, 921m, 881s, 820s, 736s.
Phase purity was confirmed by Xꢀray powder diffraction (Supporting Information).
Synthesis of {LꢁTBAI}ꢀβ
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Solutions of L (20 mg, 53 ꢁmol) and tetrabutylammonium iodide (20 mg, 54 ꢁmol) were
prepared, each dissolved in 2 mL of 5:95 methanol:ethyl acetate, and combined. The resulting
clear solution was left to evaporate to dryness, yielding a pale yellow oil which crystallised over
the course of two days. The crystalline material was triturated with ethyl acetate, and the crystals
isolated by filtration, washed with ethyl acetate, and dried in air. Yield 16 mg (40 %). m.p. 120ꢀ
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123 °C (decomp.); Found C, 40.54; H, 5.42; N, 3.58; Calculated for C H N I C, 40.13; H,
25 39 2 3
ꢀ1
5
.25; N, 3.74%; νmax (ATR, cm ) 3051w, 2959m sh, 2872m, 2154m, 1572m, 1553s, 1467m sh,
1433s, 1380m, 1287w, 1266w, 1240w, 1205m, 1149m, 1077w, 1031w, 982m, 946m, 881m sh,
21s, 739s. Phase purity was confirmed by Xꢀray powder diffraction (Supporting Information).
8
Synthesis of {L ꢁTBAFꢁMeOH}
2
Solutions of L (20 mg, 53 ꢁmol) and tetrabutylammonium fluoride trihydrate (17 mg, 54 ꢁmol)
were prepared, each dissolved in 2 mL of 5:95 methanol:ethyl acetate, and combined. The
resulting clear solution was allowed to concentrate by evaporation overnight, yielding colourless
crystals after 12 hours. The crystals were isolated by filtration, washed with ethyl acetate, and
dried in air. Yield 15 mg (42 %). m.p. 116ꢀ119 °C (decomp.); Found C, 40.27; H, 4.43; N, 3.88;
ꢀ1
Calculated for C H N OFI C, 39.98; H, 4.41; N, 4.00%; ν (ATR, cm ) 3056w, 2963m sh,
3
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46
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max
2
874m, 2823w, 2524w br, 2157m, 1574s, 1556s, 1470m, 1437s, 1380w, 1342w, 1281m, 1241m,
210m, 1155m, 1081w, 1025s, 981m, 951m, 926w, 880m sh, 805s, 732s sh. Phase purity was
1
confirmed by Xꢀray powder diffraction (Supporting Information).
Synthesis of {L (TBAF) }
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To a warmed solution of L (20 mg, 53 ꢁmol) in 2 mL of ethyl acetate was added a solution of
tetrabutylammonium fluoride trihydrate (12 mg, 38 ꢁmol) in 1 mL of ethyl acetate, causing
immediate formation of a white suspension. The solution was sealed and allowed to stand
overnight, and the resulting colourless crystals were isolated by filtration, washed with ethyl
acetate, and dried in air. Yield 17 mg (58 %). m.p. 149ꢀ153 °C (decomp.); Found C, 42.60; H,
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ꢀ1
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.95; N, 4.07; Calculated for C H N F I C, 42.70; H, 4.92; N, 4.22%; ν
(ATR, cm )
max
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3049w, 2963m sh, 2874m, 2147m, 1572m, 1552s, 1480m sh, 1436s, 1380m, 1281w, 1238m,
1209m, 1156w, 1081w, 1029w, 981m, 947m, 887w br, 815s sh, 737s sh. Phase purity was
confirmed by Xꢀray powder diffraction (Supporting Information).
Xꢀray crystallography
Structural and refinement parameters are presented in Table 1. All diffraction data were collected
using a Bruker APEXꢀII Duo dualꢀsource instrument using graphiteꢀmonochromated Mo Kα (λ =
0.71073 Å) or microfocus Cu Kα (λ = 1.54178 Å) radiation. Datasets were collected using ω and
φ scans with the samples immersed in oil and maintained at a constant temperature of 100 K
using a Cobra cryostream. The data were reduced and processed using the Bruker APEX suite of
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programs. Multiꢀscan absorption corrections were applied using SADABS. The diffraction
data were solved using SHELXT and refined by fullꢀmatrix least squares procedures using
4
9ꢀ51
2
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SHELXLꢀ2015 within the OLEXꢀ2 GUI.
The functions minimized were Σw(F ꢀF ), with
o c
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ꢀ1
2
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w=[σ (F )+aP +bP] , where P=[max(F ) +2F ]/3. All nonꢀhydrogen atoms were refined with
o
o
c
anisotropic displacement parameters. All carbonꢀbound hydrogen atoms were placed in
calculated positions and refined with a riding model, with isotropic displacement parameters
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equal to either 1.2 or 1.5 times the isotropic equivalent of their carrier atoms. Where appropriate
and as discussed in the text, the positions of hydrogen atoms involved in hydrogen bonding
interactions were refined to provide the best fit for the residual Fourier peaks and assigned a Uiso
value equal to 1.5 times that of the nearest associated atom, with the appreciation that the exact
positions of these atoms cannot be meaningfully inferred from Xꢀray diffraction data. The
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strongly hydrogenꢀbonded hydrogen atoms in the structure of {L ·TBAF·MeOH} were modelled
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to coincide with the largest Fourier residual peak between the two possible donor atoms, which
provided the best crystallographic fit (Supporting Information). However, the exact positions of
these hydrogen atoms cannot be unambiguously inferred from the Xꢀray diffraction data, nor are
their exact positions intended to be strongly implied by the model. Several of the datasets
displayed minor disorder affecting the tetrabutylammonium cations; where appropriate, the
positions of outer carbon atoms were split across multiple orientations and the occupancy of each
disordered contributor refined as a free variable, and then fixed to an appropriate value.
Restraints on bond lengths or U tensors were only employed when a meaningful improvement
ij
in the ability of the structural model to describe the true chemical behavior was obtained. Despite
repeated attempts, all isolated crystals of compound {L (TBAF) } suffered from substantial nonꢀ
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merohedral twinning and displayed poor diffraction characteristics, necessitating the use of
microfocus Cu Kα radiation for the data collection. Presumably due to the high absorption
ꢀ1
inherent to this wavelength in the presence of heavy atoms (ꢁcalc = 22.2 mm ), the crystals
suffered decomposition by beam damage after several hours of irradiation. A structure model
was obtained by merging two datasets collected before the crystal decomposition became
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2
untenable, using leastꢀsquares scaling and merging procedures in XPREP ; although the
structure model necessarily displays poor refinement statistics, the atomic connectivity is
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unambiguous and supported by FTIR, elemental analysis and Xꢀray powder diffraction data.
Particular refinement strategies for each structure, including the specific use of restraints, are
provided in the refine_special_details sections of the combined crystallographic information file.
CCDC 1480733ꢀ1480739
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Scheme 1: Synthesis of 2,6ꢀbis(iodoethynyl)pyridine L. Reagents and conditions: (i)
Trimethylsilylacetylene, CuI, Pd(PPh ) Cl , NEt , THF; (ii) silica gel, DCM/Hexane; (iii) KI,
3
2
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3
TBHP, MeOH.
Results
Synthesis and structure of 2,6ꢀbis(iodoethynyl)pyridine L
The title compound 2,6ꢀbis(iodoethynyl)pyridine L was prepared in three steps from 2,6ꢀ
dibromopyridine with an overall yield of 31% as demonstrated in Scheme 1. Single crystals of
2,6ꢀbis(iodoethynyl)pyridine L were prepared by slow cooling and evaporation of a hot ethyl
acetate solution, yielding colourless crystals within several hours. The crystals were analysed by
single crystal Xꢀray diffraction, and a structure model was generated in the orthorhombic space
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group P2 2 2 . The asymmetric unit of L contains the molecule in its entirety, with no associated
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solvent or guest molecules. The structural parameters, particularly the C≡C bond lengths of
.207(4) and 1.210(4) Å, and CꢀI bond lengths of 1.979(3) and 2.011(3) Å, are consistent with
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the expected values. The statistically significant discrepancy in lengths for the two carbonꢀiodine
bonds can be ascribed to the differences in intermolecular interactions between the two groups.
Iodine atom I1 acts as a halogen bond donor in an interaction with the pyridine nitrogen atom of
an adjacent molecule, with an I···N distance of 2.901(2) Å and angle CꢀI···N of 175.1(1)°. This
interaction most likely leads to lengthening of the CꢀI bond due to the electron donation into the
iodine σꢀhole. Conversely, due to the lack of any other available groups of significant Lewis
basicity, and crystal packing constraints preventing any possible iodineꢀiodine interactions, the
iodine atom I2 does not engage in any meaningful intermolecular interactions within the
structure, and as a consequence, exhibits the shorter of the two CꢀI bond lengths. The structure of
L is shown in Figure 1.
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Figure 1. (Top) Structure of L with heteroatom labelling scheme. (Bottom) Halogen bonding
I···N interactions in the structure of L
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The halogen bonding interaction present in L propagates a oneꢀdimensional chain parallel to
the crystallographic b axis. The interactions between adjacent chains are limited to minor πꢀπ
interactions, although the degree of overlap is limited by the undulating geometry of each chain
and the low symmetry and relatively compact πꢀsurface of each molecule of L.
Structure of {LꢁTBABr}
Reaction of L with one equivalent of tetrabutylammonium bromide in ethyl acetate gave a white
oily suspension immediately upon mixing. On standing for several hours, colourless crystals of
{L·TBABr} deposited which were isolated and subjected to single crystal Xꢀray diffraction. The
structure model obtained in the triclinic space group Pꢀ1 reveals an asymmetric unit containing
two unique molecules of L, two tetrabutylammonium cations and two associated bromide
counterions. The structure of {L·TBABr} is shown in Figure 2. Both molecules of L engage in
halogen bonding interactions with the two unique bromide ions; each of which interacts with two
iodine atoms, from crystallographically unique L molecules. The I···Br distances for these
interactions fall in the range 3.1604(4) – 3.2280(4) Å, and CꢀI···Br angles in the range 174.4(1) ꢀ
176.0(1) °. For the two unique bromide ions, the angles I···Br···I are comparable, at 77.36(1)
and 78.92(1)° for Br1 and Br2, respectively. Each of the four unique CꢀI bond lengths lie in the
range 2.021(4) – 2.037(4) Å.
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Figure 2. Structure of {L·TBABr} with heteroatom labelling scheme. Hydrogen atoms are
omitted for clarity. Symmetry codes used to generate equivalent atoms: i) 1+x, +y, +z.
The bridging connectivity of both the L molecules and bromide anions imparts a oneꢀ
dimensional polymeric character to the extended structure of {L·TBABr} in which alternating
L···Br···L chains proceed in a helical fashion parallel to the a axis. The helical nature of the
chain is imparted by the dihedral angles (measured I1ꢀI2···I3ꢀI4) of 28.485(3)° for binding to
Br1 and 27.214(3)° for binding to Br2. The helical pitch distance of 8.3829(2) Å is equivalent to
the length of the crystallographic a axis and allows for two complete molecules of L and two
bromide anions per revolution. The central cavity of each helicate is occupied by one of the two
unique tetrabutylammonium cations, while the other cation is associated with the external helical
groove. Myriad weak CꢀH··π interactions occur between these cations and the pyridine groups
comprising each helix, adding to the Coulombic attractions between the cationic and anionic
species. Permitted by the rhombic outer shape of the helices, adjacent chains pack in offset
layers, with handedness conserved along the c axis and alternating along the b axis. No
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substantial void space or solvent guest molecules were observed within the structure of
{
L·TBABr}.
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Figure 3. Top: Representation of one helical chain within the structure of {L·TBABr}.
Hydrogen atoms and tetrabutylammonium cations omitted for clarity. Bottom: Representation of
the helical chain in {L·TBABr}, rendered as spaceꢀfilling, and the relationship with the
tetrabutylammonium cations located within the helical cavity (coloured yellow), and those
associated with the external groove (coloured green).
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Synthesis and Structure of {LꢁTBACl} and {L ·TBACl}
2
The reaction of L with tetrabutylammonium chloride in ethyl acetate under similar conditions to
those employed in the synthesis of {L·TBABr} gave a similar white oily deposit on mixing,
which slowly deposited colourless microcrystals. Although the crystals obtained by this method
were not of sufficient quality to allow structure determination by single crystal Xꢀray diffraction,
both Xꢀray powder diffraction and infrared spectroscopy of the solid showed an equivalent
structure to {L·TBABr}, and microanalysis was consistent with a formulation of {L·TBACl} for
the material obtained. However, repeating the reaction in a 5% methanol:ethyl acetate solvent
system gave a clear solution on mixing of the two components, which deposited large colourless
crystals after concentrating by evaporation overnight. Analysis of the crystals by single crystal
Xꢀray diffraction provided a structural model of {L ·TBACl} in the triclinic space group Pꢀ1.
2
The asymmetric unit contains two complete molecules of L, with one chloride ion and associated
tetrabutylammonium cation. Both molecules of L are geometrically equivalent within error, and
differ only by their relative orientations. Interestingly, no evidence of the helicate phase was
observed when carrying out the reaction in this solvent system, regardless of whether a 1:1 or 2:1
L:TBACl ratio was used.
Here, the chloride ion is engaged in halogen bonding interactions with each of the four unique
iodine atoms, at Cl···I distances in the range 3.0839(5) – 3.1196(5) Å in an approximately
squareꢀplanar geometry. The geometry of these interactions is surprisingly regular, with all
I···Cl··I cis angles falling within the range 83.424(12) – 94.506(15)° and the two trans angles
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62.27(2)° and 164.32(2)° demonstrating a slight deviation from planarity, consistent with the
Cl···(I mean plane) distance of 0.45 Å. The structure of {L ·TBACl} is shown in Figure 4.
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Figure 4. Structure of the repeating unit of {L ·TBACl} with heteroatom labelling scheme.
2
Hydrogen atoms are omitted for clarity. Symmetry codes used to generate equivalent atoms: i)
+x, ꢀ1+y, ꢀ1+z.
With each chloride ion acting as a fourꢀconnected node, the extended structure of {L ·TBACl}
2
consists of a oneꢀdimensional chain comprised of planar L Cl loops; oriented parallel to the
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[0,1,1] vector. The chains are grouped into pairs through offset faceꢀtoꢀface πꢀπ interactions on
one face, with minimum interatomic distance 3.359(3) Å for C4···C16, while the opposite face is
interrupted by layers of tetrabutylammonium cations. Each loop is defined by two inwardsꢀ
directed pyridine nitrogen atoms separated by 8.195(3) Å; these loops are occupied by two butyl
chains of the nearby tetrabutylammonium cations. In the orthogonal direction, the chains align in
an offset edgeꢀtoꢀedge fashion to give a densely packed layered structure as shown in Figure 5.
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Figure 5. The extended structure of {L ·TBACl}, viewed perpendicular (top) and nearꢀparallel
2
(bottom) to the direction of propagation. Hydrogen atoms are omitted for clarity.
Structure of {LꢁTBAI}ꢀα
Combining L with a suspension of tetrabutylammonium iodide in ethyl acetate, followed by
heating at reflux for 30 minutes to account for the low room temperature solubility of the iodide
salt, gave a white suspension after cooling to room temperature, which slowly crystallised on
standing overnight. Analysis of the colourless crystals by single crystal Xꢀray diffraction
provided a structural model in the orthorhombic space group Pccn. Equivalent crystals could also
be prepared, albeit containing unreacted tetrabutylammonium iodide as an impurity, by mixing
the two components at room temperature, equivalent to the procedure used for the bromide and
chloride adducts. The asymmetric unit of {L·TBAI}ꢀα contains one molecule of L, one iodide
anion and halves of two nonꢀequivalent tetrabutylammonium cations. The iodide anions act as
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acceptors for two halogen bonding interactions originating from the iodoalkyne groups of L, at
I···I distances 3.3654(5) and 3.4027(5) Å for I1···I3 and I2···I3, respectively. The I···I···I angle
of 80.338(12) is intermediate between the equivalent angles in {L·TBABr} and {L ·TBACl}.
2
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However, unlike the extended chains observed in those systems, in {L·TBAI}ꢀα two iodide ions
act as caps to form a discrete cyclic assembly of the form L I . These assemblies adopt a saddleꢀ
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type geometry, with a 49° angle between the mean planes of the two pyridine rings. Similarly to
the previous cases, these loops encapsulate a tetrabutylammonium cation within the internal
volume, defined by a distance between inwardsꢀfacing pyridine nitrogen atoms of 8.155(8) Å.
Unlike the case of {L ·TBACl}, however, the cation is centred on the pocket with butyl chains
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extending outwards, rather than occupying the central volume with butyl chains from an external
position. The remaining tetrabutylammonium cation resides in a poorlyꢀlocalised position on the
periphery of the assembly, electrostatically bound by the nearby iodide anions. The difference in
cation ordering between the encapsulated and free tetrabutylammonium groups can be seen by
comparing the average freely refined U values for the carbon and nitrogen atoms of each
eq
cation, which increases from 0.036 for the encapsulated cation to 0.124 for the unconfined. No
meaningful disorder model could be beneficially applied to this group, and so the atom sites were
allowed to freely refine at full occupancy with no ADP restraints to provide the most realistic
depiction of the poorly localised group.
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Figure 6. The structure of {L·TBAI}ꢀα with heteroatom labelling scheme. Hydrogen atoms are
omitted for clarity. Symmetry codes used to generate equivalent atoms: i) 3/2ꢀx, 1/2ꢀy, +z.
Interestingly, when viewed parallel to the crystallographic c axis, the largeꢀscale structure of
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{
L·TBAI}ꢀα bears a striking resemblance to the helical assembly of {L·TBABr}. The L2I2
assemblies align into columns parallel to the c axis, with a distance of 8.1407(3) Å between
equivalent iodide anions comparable to the helical pitch of 8.3829(2) Å observed in {L·TBABr}.
The rhombic shape and offset layer packing of the columns is also comparable between the two
compounds, as is the alignment of the tetrabutylammonium cations. The two structures can be
contrasted only by considering the relative twisting of each pair of L molecules within an
essentially fixed matrix of tetrabutylammonium halides, as is demonstrated in Figure 7.
Figure 7. Overlaid structures of {L·TBABr} (yellow) and {L·TBAI}ꢀα (red) using the halide
ions as anchor points.
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Structure of {LꢁTBAI}ꢀβ
Given the similarities between {L·TBAI}ꢀα and {L·TBABr}, the reaction between L and
tetrabutylammonium iodide was repeated under conditions comparable to those which formed
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{
L ·TBACl}, to test for the presence of any other phases with different packing motifs. Reaction
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of L with tetrabutylammonium iodide in a solution of 5% methanol in ethyl acetate gave a clear
solution on mixing, from which colourless crystals deposited after concentration by evaporation
overnight. Analysis of these crystals by single crystal Xꢀray diffraction gave a structure model
for {L·TBAI}ꢀβ in the triclinic space group Pꢀ1, with an asymmetric unit containing two
molecules of L, two iodide ions, and two tetrabutylammonium cations. The halogen bonding
connectivity of {L·TBAI}ꢀβ is directly comparable to that observed in the α phase, in that two L
molecules and two iodide anions comprise a cyclic assembly with I···I distances in the range
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.3090(3) – 3.4052(3) Å and I···I···I angles 74.506(6)° and 77.026(6)° for I5 and I6,
respectively. The halogenꢀbonded macrocycles in the β phase are more planar than those in the α
phase, with an angle between pyridine mean planes of 36° in the β phase compared to 49° in the
α phase. The distance between the inwardsꢀfacing pyridine nitrogen atoms from each loop is
reduced by ca. 0.5 Å in the β phase, to a value of 7.617(4) Å, and consequently only a single
butyl chain from one tetrabutylammonium cation is observed occupying the free volume within
each loop.
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Figure 8. Top: The asymmetric unit of {L·TBAI}ꢀβ with heteroatom labelling scheme.
Hydrogen atoms are omitted for clarity. Bottom: Overlaid structures of the α (red) and β (blue)
phases of {L·TBAI}.
Adjacent loops are aligned in a cornerꢀtoꢀcorner fashion in the [1,1,0] direction, with a distance
of 5.1194(3) Å between iodide anions. The extended structure of {L·TBAI}ꢀβ bears a
resemblance to that of {L ·TBACl} in this respect, where iodide anions alternate between
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halogen bonding L linkages and no linking interactions, rather than the continuous chain formed
in the chloride case, as is evident from Figure 9. The arrangement of these chains relative to one
another was also similar to that observed in {L ·TBACl}, with lateral groups oriented
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approximately parallel to one another and forming an undulating 2ꢀdimensional layer,
interspersed by layers of tetrabutylammonium cations. Intermolecular interactions in the
structure of {L·TBAI}ꢀβ are largely limited to various CꢀH···π interactions between the
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tetrabutylammonium cations and the L moieties. Attempts were made to induce the formation of
an isostructural chain to {L ·TBACl} using tetrabutylammonium iodide at other stoichiometries,
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however the α and β phases of the cyclic species were the only crystalline materials isolated.
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Figure 9. Extended structure of {L·TBAI}ꢀβ showing the offset packing between adjacent
macrocycles. Hydrogen atoms are omitted for clarity.
Structure of {L ꢁTBAFꢁMeOH}
2
The reaction of L with tetrabutylammonium fluoride in 5% methanol/ethyl acetate gave
colourless crystals after concentration by slow evaporation. Analysis of the crystals by single
crystal Xꢀray diffraction provided a structural model in the triclinic space group Pꢀ1. The
asymmetric unit of {L ·TBAF·MeOH} contains four unique molecules of L, two fluoride
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anions, two tetrabutylammonium cations and two methanol molecules. Most strikingly, a strong
hydrogen bonding interaction can be seen between the fluoride ions and the methanol molecules,
with F··O distances 2.504(3) and 2.511(3) Å for the two unique interactions. The position of the
hydrogen atom in this interaction cannot be unambiguously determined by Xꢀray diffraction
techniques, particularly due to the presence of heavy atoms nearby. Nonetheless, the large
residual Fourier peaks between the pairs of F··O atoms reside consistently closer to the midꢀ
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point between the possible donors than the corresponding O site, seemingly consistent with an
F···H···O ionic hydrogen bonding mode rather than either extreme case of OꢀH···F or FꢀH···O.
A notable improvement in refinement statistics was obtained by modelling this hydrogen atom to
coincide with the Fourier residual located partꢀway between the two atoms, rather than adopting
a calculated position bonded to either of the possible donors (See Supporting Information).
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Infrared spectroscopy of the material shows a very broad absorbance in the range 3500ꢀ2400
ꢀ1
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cm with maximum ca. 2500 cm , consistent with an ionic hydrogen bonding interaction.
Repeating the reaction with CD OD in the place of methanol within the solvent mixture effected
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a detectable shift of the symmetric CH stretching band from 2822 cm to 2062 cm for the CD
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equivalent. However, due to the highly hygroscopic nature of the starting material and reaction
conditions no meaningful difference in the hydrogenꢀbonded stretching frequency was observed.
While methanolꢀfluoride adducts have been studied theoretically and in the gas and solution
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phases,
typically as clusters with multiple hydrogen bond donors, structurally characterised
examples of discrete [F···H···OMe] anions are less common. Such species can exist in the
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presence of supporting polydentate hydrogen bonding hosts or coordinated to metal ions,
but
to our knowledge {L ·TBAF·MeOH} is unique as a crystallographically characterised example
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of such an adduct supported purely by halogen bonding interactions.
The strongly hydrogenꢀbonded [F···H···OMe] anionic species act as halogen bond acceptors
within the structure of {L ·TBAF·MeOH}, with each anionic unit interacting with four iodine
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atoms, two per fluoride ion and two per oxygen atom (Figure 10). Each of the four unique F···I
distances lie in the range 2.585(2) – 2.595(2) Å, while the four O···I interactions exhibit slightly
longer distances, in the range 2.725(2) – 2.751(2) Å. The I···F···I and I···O···I angles are
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comparable, with values of 119.56(7)°, 120.38(7)°, 114.73(8)° and 115.44(8)° for the two pairs
of angles involving F and O acceptors, respectively.
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Figure 10. Top: One of the two crystallographically unique looped motifs in the structure of
{L ·TBAF·MeOH} with partial atom labelling scheme; Bottom: extended structure of the
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polymeric chain in {L ·TBAF·MeOH} showing the associated tetrabutylammonium cation.
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Hydrogen atoms are omitted for clarity. Symmetry codes used to generate equivalent atoms: i)
+x, yꢀ1, +z; ii) +x, y+1, +z.
With each F···H···OMe anion interacting with four iodine atoms, the extended structure of
{
L ·TBAF·MeOH} consists of a series of oneꢀdimensional looped chains oriented parallel to the
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b axis, resembling those observed in the structure of {L ·TBACl}. The polyatomic nature of the
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halogen bond accepting anionic species in {L ·TBAF·MeOH} lends a stepped property to each
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chain in the c direction, with the two facing L units no longer occupying coplanar orientations
across the breadth of the chains. The loops defined by these groups, with distances between
pyridine nitrogen atoms of 7.306(4) and 7.257(4) Å for the two unique pairs, are occupied by
butyl chains from nearby tetrabutylammonium cations. The longꢀrange structure of
{L ·TBAF·MeOH} is also closely related to that of {L ·TBACl}, with chains aligned in an
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offset parallel fashion in the b direction and combined into alternating doubleꢀlayers of anionic
chains and tetrabutylammonium cations in the a direction.
Structure of {L (TBAF) }
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2
Reaction of L with tetrabutylammonium fluoride in pure ethyl acetate gave a white suspension
immediately on mixing, and colourless crystals were deposited after the mixture was allowed to
stand at room temperature overnight. Despite numerous attempts to optimise the crystallisation
of this material, every crystalline batch examined suffered from severe nonꢀmerohedral twinning
and displayed poor diffraction characteristics. As such, the only sensible data collection strategy
required the use of microfocus Cu Kα radiation, which subsequently caused beam damage to the
crystals within several hours of irradiation, presumably due to the particularly high absorption
expected due to the presence of multiple heavy atoms. A connectivity model was established by
merging datasets from two partial collections, providing a structural model of unambiguous
connectivity, but nonetheless we refrain from a detailed analysis of interatomic distances or
angles due to the difficulties with data quality. Analysis of the material by Xꢀray powder
diffraction, elemental analysis and ATRꢀIR spectroscopy all strongly corroborate the suggested
structure. The asymmetric unit of {L (TBAF) }, solved and refined in the monoclinic space
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group P2 /c, contains three unique molecules of L, two fluoride anions, and two associated
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tetrabutylammonium cations. Unlike the case of {L ·TBAF·MeOH}, no solvent molecules or
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guests were detected within the structure.
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Two different modes of halogen bonding interactions take place in the structure of {L (TBAF) },
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shown in Figure 11. One fluoride atom F1 engages in two halogen bonding interactions with one
unique L group within the structure, interacting with the two unique iodine atoms at F···I
distances of 2.40(2) and 2.47(2) Å and I···F···I angle of 113.9(7)°. Fluorine atom F2 participates
in four halogen bonding interactions, involving each of the four iodine atoms from the remaining
two of the three unique L groups within the asymmetric unit. The geometry of halogen bond
donors around F2 is best described as trigonal pyramidal, in which three iodine atoms I3, I5 and
I6 define the basal plane, at F···I distances 2.531(13), 2.613(13) and 2.591(13) Å respectively,
and a distance F···(I mean plane) of 0.51 Å. The axial I···F distance is marginally longer at
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.689(13) Å, and the corresponding F···I vector is nearꢀparallel to the normal vector of the I3
basal plane (angle 1.1(3)°). These interꢀatomic distances are considerably shorter than those
observed in the structure of {L ·TBAF·MeOH}, although the larger estimated standard
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deviations must be considered. The relative shortening of the interꢀatomic distances in the case
of F1 compared to F2 is most likely a consequence of the low coordination number and the
increased efficiency of electron donation as a result.
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