Extended Self-complementary Halogen Bonded Dimers

Article abstract of DOI:10.1007/s10870-015-0616-9

The X-ray structure of a series of 1,4-diethynylbenzene bridged pyridyl polyfluoroiodo- and polyfluorobromophenyls designed to form self-complementary dimers in the solid state are reported. The compound 2-[[4-[(3-bromotetrafluorophenyl)ethynyl]phenyl]eth

Full text of DOI:10.1007/s10870-015-0616-9

J Chem Crystallogr (2015) 45:466–475
DOI 10.1007/s10870-015-0616-9
ORIGINAL PAPER
Extended Self-complementary Halogen Bonded Dimers
Lisa M. Kirchner1 Nathan P. Bowling2 Eric Bosch1
•
•
Received: 7 August 2015 / Accepted: 2 November 2015 / Published online: 17 November 2015
Ó Springer Science+Business Media New York 2015
Abstract The X-ray structure of a series of 1,4-di-
ethynylbenzene bridged pyridyl polyfluoroiodo- and
polyfluorobromophenyls designed to form self-complemen-
tary dimers in the solid state are reported. The compound
2-[[4-[(3-bromotetrafluorophenyl)ethynyl]phenyl]ethynyl]
pyridine, 1, crystalized in the triclinic space group P-1
102.6180(10)° and featured a C–HÁÁÁN hydrogen bonded
dimer.
Graphical Abstract The formation of self-complemen-
tary halogen bonded dimers with a series of 1,4-di-
ethynylbenzene bridged pyridyl polyfluoroiodo- and
polyfluorobromophenyls is reported.
˚
with unit cell parameters a = 6.3332(4) (A), b =
˚
˚
7.4288(4) (A), c = 17.8897(10) (A) and a = 91.0980
(10)°, b = 90.8580(10)° and c = 94.3830(10)°. The
asymmetric unit contains a unique molecule as a self-com-
plementary halogen bonded dimer. Compounds 2, 3-[[4-[(2-
bromotetrafluorophenyl)ethynyl]phenyl]ethynyl]pyridine and
3, 3-[[4-[(2-iodotetrafluorophenyl)ethynyl]phenyl]ethynyl]
pyridine both crystalized in the triclinic space group P-1 and
are isostructural with unit cell parameters a = 6.1324(13)
˚
˚
˚
(A), b = 11.264(2) (A), c = 13.064(3) (A), a = 66.646(3)°,
b = 89.736(3)°, c = 87.726(3)° for 2 and a = 6.1671(5)
˚
˚
˚
(A), b = 11. 2571(9) (A), c = 13.3083(11) (A), a =
66.2870(10)°, b = 88.1990(10)°, c = 87.3820(10)° for 3. In
both structures the molecules assemble as essentially planar
self-complementary halogen bonded dimers. In contrast
3-[[4-[(2-bromo-4,5-difluorophenyl)ethynyl]phenyl]ethynyl]
pyridine, 4, crystalized in the monoclinic space group P21/c
Keywords Halogen bonding Á Self-complementary Á
Dimer
˚
with unit cell parameters a = 18.7881(7) (A), b =
Introduction
˚
˚
3.83820(10) (A), c = 22.9321(9) (A), a = c = 90°, b =
Halogen bonding is now widely recognized as a useful tool in
molecular recognition and the field of crystal engineering [1].
In this context we recently reported examples of self-com-
plementary halogen bonded dimer formation with a series of
polyfluoroiodo- and polyfluorobromophenylethynylpyridi-
nes [2]. The basic plan in that research was to prepare simple
molecules containing both a pyridyl moiety as halogen bond
acceptor and fluorine activated bromo or iodo halogen bond
donor with a geometric arrangement that would favor dimer
formation. van der Boom and co-workers had earlier
& Eric Bosch
ericbosch@missouristate.edu;
http://chemistry.missouristate.edu/EricBosch.aspx
1
Chemistry Department, Missouri State University, 901 South
National Avenue, Springfield, MO 65897, USA
2
Department of Chemistry, University of Wisconsin-Stevens
Point, 2001 Fourth Avenue, Stevens Point, WI 54481, USA
123

J Chem Crystallogr (2015) 45:466–475
467
established that 4-[(4-bromo-2,3,5,6-tetrafluorophenyl)
ethynyl]pyridine forms one-dimensional halogen bonded
ribbons of molecules [3, 4] and that 3,5-diiodo-2,4,6-triflu-
orostilbazole which does not have a linear arrangement of the
donor and acceptor sites formed infinite helices [4]. In contrast
we demonstrated that a simple positional switch led to the
exclusive formation of self-complementary halogen-bonded
dimers. For example, 3-[(2-bromo-3,4,5,6-tetrafluorophenyl)
ethynyl]pyridine favored formation of the self-complementary
dimer in the solid state as shown in Scheme 1 [2].
anhydrous sodium sulfate and the solvent evaporated. The
crude product was purified using flash chromatography
with silica gel primed with hexanes and eluted with a
progressively polar eluant comprising mixtures of hexanes
with ethyl acetate. Fractions were evaluated using TLC
(2:1 hexanes:ethyl acetate mix). The fractions containing
the desired compound were collected and the solvent
evaporated. The product was a pale yellow solid (2.639 g,
41 %). 1H NMR (CDCl3, 400 MHz):
d 8.63 (d,
J = 3.9 Hz, 1H), 7.70 (dt, J = 7.6, 1.9 Hz, 2H), 7.66 (dd,
J = 6.1, 1.8 Hz, 1H), 7.52 (d, J = 7.8 Hz, 1H), 7.32 (td,
J = 8.5, 1.9 Hz, 2H), 7.25 (ddd, J = 12.3, 2.7, 1.2 Hz,
1H). 13C NMR (100 MHz): 150.1, 143.1, 137.6, 136.2,
133.4, 127.2, 123.0, 121.7, 95.2, 89.9, 88.1.
In this short paper we report the extension of that study
to include the series of 1,4-diethynylbenzene bridged pyr-
idyl polyfluoroiodophenyl and polyfluorobromophenyls
shown in Scheme 2.
Synthesis of 2-[(4-Ethynylphenyl)ethynyl]pyridine, 6
Experimental Section
Trimethylsilyacetylene (1.601 g, 16 mmol), 2-[(4-iodophe-
nyl)ethynyl]pyridine 5 (2.559 g, 8.4 mmol), and triethy-
lamine (40 ml) were stirred under argon for ten minutes
Synthesis of 2-[(4-Iodophenyl)ethynyl]pyridine, 5
A mixture of 2-ethynylpyridine (2.193 g, 21 mmol), 1,4-
diiodobenzene (8.095 g, 25 mmol) and triethylamine
(40 ml) were stirred under argon for ten minutes while
palladium(II) bis(triphenylphosphine)dichloride (117 mg,
0.14 mmol) and copper(I) iodide (36 mg, 0.17 mmol) were
added. The mixture was stirred under the inert atmosphere
for two days at room temperature. The reaction mixture
was dissolved in dichloromethane (200 ml) and washed
twice with water (100 ml). The solution was dried over
while
palladium(II)
bis(triphenylphosphine)dichloride
(121 mg, 0.14 mmol) and copper(I) iodide (19 mg, 0.09
mmol) were added. The mixture was stirred under the inert
atmosphere for two days at room temperature. The reaction
mixture was dissolved in dichloromethane (200 ml) and
washed twice with water (100 ml). The solution was dried
over anhydrous sodium sulfate and the solvent evaporated.
The crude product was purified using flash chromatography
as described for compound 5. The TMS-protected interme-
diate crystalized as colorless needles from ethyl acetate
1
(1.366 g, 59 %). H NMR (CDCl3, 400 MHz): d 8.63 (d,
J = 4.9 Hz, 1H), 7.69 (td, J = 7.8, 1.8 Hz, 1H), 7.53 (m, J =
8.0 Hz, 3H), 7.45 (br d, J = 6.5 Hz, 2H), 7.26 (m, 1H), 0.261
(s, 9H). 13C NMR (100 MHz): 152.36, 148.86, 138.52,
132.08, 131.58, 123.63, 123.16, 122.60, 120.33, 104.52, 96.79,
92.33, 87.85, 0.10.
The TMS-protected intermediate (1.2331 g, 4.5 mmol)
was added to a solution of potassium hydroxide (2.727 g)
in absolute ethanol (100 ml) and the resultant mixture
stirred at room temperature for 1 h and then poured into DI
Scheme 1 Self-complementary halogen bonded dimers [2]
Scheme 2 Target molecules
used in this study
123

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J Chem Crystallogr (2015) 45:466–475
water (100 ml). The mixture was extracted with dichlor-
omethane (200 ml), washed once more with DI water
(70 ml). The solution was dried over anhydrous sodium
sulfate and the solvent was evaporated to yield 6 as a
were added. The mixture was stirred under the inert atmo-
sphere for two days at room temperature. The reaction
mixture was dissolved in dichloromethane (200 ml) and
washed twice with water (100 ml). The solution was dried
over anhydrous sodium sulfate and the solution was evap-
orated. The crude product was purified using flash chro-
matography with silica gel primed with hexanes and a
progressively polar eluant, ethyl acetate. Fractions were
evaluated using TLC (2:1 hexanes:ethyl acetate mix). The
fractions containing the desired compound were collected
and the solvent was evaporated. The product was a peach
colored flaky solid (1.4378 g, 63 %). 1H NMR (CDCl3,
400 MHz): d 8.76 (d, J = 1.4 Hz, 1H), 8.56 (dd, J = 1.4,
4.7 Hz, 1H), 7.80 (dt, J = 8.0, 2.0 Hz, 1H), 7.72 (md,
J = 8.3 Hz, 2H), 7.31 (ddd, J = 8.8, 4.9 Hz, 0.78 Hz 1H),
7.27 (m, 2H). 13C NMR (100 MHz): 152.2, 148.8, 138.5,
137.7, 133.1, 123.1, 122.1, 120.2, 94.9, 91.7, 87.3.
1
creamy-white solid (0.6479 g, 71 %). H NMR (CDCl3,
400 MHz): d 8.64 (br d, J = 4.9 Hz, 1H), 7.69 (td,
J = 7.6, 1.9 Hz, 1H), 7.55 (m, 3H), 7.48 (md, J = 6.6 Hz,
2H), 7.26 (m, 1H), 3.19 (s, 1H). 13C NMR (100 MHz):
150.1, 143.1, 136.2, 132.1, 131.9, 127.2, 122.9, 122.7,
122.6, 90.3, 88.5, 83.1, 79.2.
Synthesis of 2-[[4-[(3-Bromotetrafluorophenyl)
ethynyl]phenyl]ethynyl]pyridine, 1
A
mixture of 2-[(4-ethynylphenyl)ethynyl]pyridine
(0.4043 g, 1.99 mmol), 1,3-dibromotetrafluorobenzene
(0.7948 g, 2.5 mmol) and triethylamine (15 ml) were stir-
red under argon for ten minutes while palladium(II)
bis(triphenylphosphine)dichloride (66.5 mg, 0.07 mmol)
and copper(I) iodide (16.9 mg, 0.07 mmol) were added.
The mixture was stirred under the inert atmosphere for
seven days at 85 °C. The reaction mixture was dissolved in
dichloromethane (100 ml) and washed twice with water
(50 ml). The solution was dried over anhydrous sodium
sulfate and the solvent evaporated. The crude product was
purified using flash chromatography with silica gel primed
with hexanes and eluted with a progressively polar eluant
comprising mixtures of hexanes with ethyl acetate. Frac-
tions were evaluated using TLC (2:1 hexanes:ethyl acetate
mix). The fractions containing the desired compound
were collected and the solvent evaporated. The product
was crystallized in a screw-capped vial from CDCl3 as
colorless needles (0.2538 g, 30 %). Melting point =
177.1–179.3 °C. 1H NMR (CDCl3, 400 MHz): d 8.63 (br d,
J = 4.9 Hz, 1H), 7.69 (dt, J = 7.6, 1.8 Hz, 1H), 7.53 (md,
J = 8.0 Hz, 3H), 7.45 (md, J = 8.0 Hz, 2H), 7.26 (m, 1H).
19F NMR (376 MHz): -161.2 (td, J = 21.8, 9.2 Hz, 1F),
-129.4 (dd, J = 21.2, 5.7 Hz, 1F), -123.0 (dd, J = 21.8,
5.8 Hz, 1F), -105.4 (d, J = 9.1 Hz, 1F). 13C NMR
(100 MHz): 155.2 (md, J = 253 Hz), 150.5 (md, J =
255 Hz), 150.2, 149 (md, J = 255 Hz), 143.1, 137.5 (md,
J = 248 Hz), 136.3, 134.5 (m, J = 7 Hz), 132.1, 131.9,
128.1 (m, J = 5.0 Hz), 127.3, 123.5, 123.1, 122.1, 100.6
(d, J = 3.7 Hz), 95.3 (t, J = 3.0 Hz), 90.9, 88.4.
Synthesis of 3-[(4-Ethynylphenyl)ethynyl]pyridine, 8
Trimethylsilylacetylene (0.633 g, 6.4 mmol), 3-[(4-iodo-
phenyl)ethynyl]pyridine 7 (1.389 g, 4.6 mmol), and tri-
ethylamine (30 ml) were stirred under argon for ten minutes
while palladium(II) bis(triphenylphosphine)dichloride
(156 mg, 0.18 mmol) and copper(I) iodide (29 mg,
0.14 mmol) were added. The mixture was stirred under the
inert atmosphere for two days at room temperature. The
reaction mixture was dissolved in dichloromethane (200 ml)
and washed twice with water (100 ml). The solution was
dried over anhydrous sodium sulfate and the solvent was
evaporated. The crude product was purified using flash
chromatography with silica gel as described before. The
TMS protected intermediate was isolated as a pale yellow
1
solid (1.366 g, 86 %). H NMR (CDCl3, 400 MHz): d 8.76
(br d, J = 1.4 Hz, 1H), 8.56 (dd, J = 4.9, 1.8 Hz, 1H), 7.80
(dt, J = 7.6, 1.9 Hz, 1H), 7.47 (m, 4H), 7.29 (ddd,
J = 8.0 Hz, 4.9 Hz, 1.0 Hz, 1H) 0.22 (s, 9H). 13C NMR
(100 MHz): 152.4, 148.9, 138.5, 132.1, 131.6, 123.6, 123.2,
122.6, 120.3, 104.5, 96.8, 92.3, 87.9, 0.10.
The TMS protected intermediate (0.994 g, 3.6 mmol)
was added to a solution of potassium hydroxide (2.816 g)
in absolute ethanol (100 ml) and stirred at room tempera-
ture for 1 h. The reaction mixture was then poured into DI
water (100 ml) and extracted with dichloromethane
(200 ml). The organic solution was washed with DI water
(70 ml). The solution was dried over anhydrous sodium
sulfate and the solvent evaporated to yield the desired
product as a brown solid (0.674 g, 92 %). 1H NMR
(CDCl3, 400 MHz): d 8.78 (s, 1H), 8.56 (brd, J = 4.9 Hz,
1H), 7.81 (dq, J = 7.8 Hz, 1.7 Hz, 1H), 7.53 (m, 4H), 7.30
(m, 1H), 3.20 (s, 1H). 13C NMR (100 MHz): 152.3, 148.8,
138.5, 132.5, 132.2, 131.6, 128.6, 123.1, 122.5, 92.0, 87.3,
83.1, 79.2.
Synthesis of 3-[(4-Iodophenyl)ethynyl]pyridine, 7
A mixture of 3-ethynylpyridine (0.9683 g, 9.4 mmol), 1,4-
diiodobenzene (3.2908 g, 10 mmol) and triethylamine
(40 ml) were stirred under argon for ten minutes while
palladium(II) bis(triphenylphosphine)dichloride (125.3 mg,
0.15 mmol) and copper(I) iodide (26.2 mg, 0.13 mmol)
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J Chem Crystallogr (2015) 45:466–475
469
Synthesis of 3-[[4-[(2-Bromotetrafluorophenyl)ethynyl]
phenyl]ethynyl]pyridine, 2
NMR (376 MHz): -153.8 (td, J = 20.5 Hz, 4.0 Hz, 1F),
-151.0 (ddd, J = 23 Hz, 19 Hz, 1F), -130.4 (ddd,
J = 20.7 Hz, 10 Hz, 4.0 Hz, 1F), -113.4 (ddd,
J = 22.5 Hz, 10 Hz, 4.0 Hz, 1F). 13C NMR (100 MHz):
152.3, 148.9, 147.4 (dm, J = 256 Hz), 138.6–148.0 (3
signals, each dm, J = *250 Hz), 138.5, 131.8, 131.2,
134.3 (m), 127.8 (m), 123.8, 123.1, 121.9, 120.1, 99.7,
92.0, 88.5, 84.7.
A
mixture of 3-[(4-ethynylphenyl)ethynyl]pyridine
8
(0.276 g, 1.4 mmol), 1,2-dibromotetrafluorobenzene
(0.696 g, 2.3 mmol) and triethylamine (15 ml) were stirred
under argon for ten minutes while palladium(II) bis(triph-
enylphosphine)dichloride (56 mg, 0.06 mmol) and cop-
per(I) iodide (15 mg, 0.07 mmol) were added. The mixture
was stirred under the inert atmosphere for seven days at
85 °C. The reaction mixture was dissolved in dichlor-
omethane (100 ml) and washed twice with water (50 ml).
The solution was dried over anhydrous sodium sulfate and
the solution was evaporated. The crude product was puri-
fied using flash chromatography as described before.
Fractions were evaluated using TLC (2:1 hexanes:ethyl
acetate mix). The desired compound was crystallized from
ethyl acetate as flat, clear crystals (0.144 g, 16 %). Melting
Synthesis of 3-[[4-[(2-Bromo-4,5-difluorophenyl)
ethynyl]phenyl]ethynyl]pyridine, 4
A
mixture of 3-[(4-ethynylphenyl)ethynyl]pyridine 8
(0.2726 g, 1.3 mmol), 1,2-dibromo-4,5-difluorobenzene
(0.4948 g, 1.8 mmol) and triethylamine (10 ml) were stir-
red under argon for ten minutes while palladium(II)
bis(triphenylphosphine)dichloride (78 mg, 0.08 mmol) and
copper(I) iodide (24 mg, 0.11 mmol) were added. The
mixture was stirred under the inert atmosphere for seven
days at 85 °C. The reaction mixture was dissolved in
dichloromethane (100 ml) and washed twice with water
(50 ml). The solution was dried over anhydrous sodium
sulfate and the solution was evaporated. The crude product
was purified using flash chromatography as described
above. The product was crystallized from CDCl3 as clear
plates (0.258 g, 51 %). Melting point = 183.0–185.6 °C.
1H NMR (CDCl3, 400 MHz): d 8.78 (br s, 1H), 8.57 (d,
J = 4.0 Hz, 1H), 7.81 (d, J = 7.8 Hz, 1H), 7.54 (m, 4H),
7.44 (mt, J = 8.5 Hz, 1H), 7.37 (mt, J = 8.3 Hz, 1H), 7.39
(m, 1 H). 19F NMR (376 MHz): -137.8 (ddd, J = 21.2,
10.3, 7.5 Hz, 1F), -132.5 (dt, J = 21.2, 8.8 Hz, 1F). 13C
NMR (100 MHz): 152.2, 150.0 (dd, J = 258, 13.7 Hz),
149.2 (dd, 250, 12.5 Hz), 148.8, 138.4, 134.9 (m,
J = 5.9 Hz), 131.7, 131.6, 130.1, 127.9 (m), 123.1 (d,
J = 20.6 Hz), 122.6, 121.8, 120.1, 119.9 (d, J = 20.3 Hz),
93.9, 92.1, 88.2, 88.0.
1
point = 164.7–167.3 °C. H NMR (CDCl3, 400 MHz): d
8.78 (brdd, J = 2.1, 0.8 Hz, 1H), 8.57 (dd, J = 4.9,
1.8 Hz, 1H), 7.82 (dt, J = 8.0, 2.0 Hz, 1H), 7.58 (m, 4H),
7.33 (m, 1H). 19F NMR (376 MHz): -155.3 (td,
J = 22.5 Hz, 3.0 Hz, 1F), -151.5 (td, J = 21.8, 3.4 Hz,
1F), -132.1 (ddd, J = 21.3 Hz, 9.5 Hz, 3.5 Hz, 1F),
-128.2 (ddd, J = 21.8 Hz, 9.2 Hz, 3.5 Hz, 1F). 13C NMR
(100 MHz): 152.3, 148.9, 148.5 (dm, J = 252 Hz), 145.8
(dddd, J = 248 Hz, 12 Hz, 4.8 Hz, 2.5 Hz), 141.3 (dddd,
J = 260 Hz, 18 Hz, 13.3 Hz, 3.2 Hz), 140.1 (dddd,
J = 260 Hz, 16 Hz, 12.8 Hz, 3.8 Hz), 138.5, 134.8, 134.5,
133.0, 131.5 (m), 129.1, 127.7 (m), 123.8, 120.1, 100.6 (d,
J = 5.2 Hz), 91.9, 88.5, 81.1.
Synthesis of 3-[[4-[(2-Iodotetrafluorophenyl)
ethynyl]phenyl]ethynyl]pyridine, 3
A
mixture of 3-[(4-ethynylphenyl)ethynyl]pyridine
8
(0.326 g, 1.6 mmol), 1,2-diiodotetrafluorobenzene
(0.810 g, 2.0 mmol) and triethylamine (10 ml) were stirred
under argon for ten minutes while palladium(II) bis(triph-
enylphosphine)dichloride (88 mg, 0.09 mmol) and cop-
per(I) iodide (20 mg, 0.09 mmol) were added. The mixture
was stirred under the inert atmosphere for seven days at
room temperature. The reaction mixture was dissolved in
dichloromethane (100 ml) and washed twice with water
(50 ml). The solution was dried over anhydrous sodium
sulfate and the solution evaporated. The crude product was
purified using flash chromatography as described above.
The product was crystalized from CDCl3 as clear plates
(0.163 g, 21 %). Melting point = 226.2–228.9 °C. 1H
NMR (CDCl3, 400 MHz): d 8.79 (d, J = 1.6 Hz, 1H), 8.59
(dd, J = 4.8 Hz, 1.6 Hz, 1H), 7.83 (dt, J = 7.8 Hz,
2.1 Hz, 1H), 7.63 (m, 2H), 7.58 (m, 2H), 7.32(m, 1H). 19F
X-ray Structure Determination
For each complex a single crystal was mounted on a
Kryoloop using viscous hydrocarbon oil. Data were col-
lected using a Bruker Apex2 CCD diffractometer equipped
˚
with Mo Ka radiation with k = 0.71073 A. Data collection
at 100 K was facilitated by use of a Kryoflex system with
an accuracy of 1 K. Initial data processing was carried
out using the Apex II software suite [5]. Structures were
solved by direct methods using SHELXS-2013 and refined
against F2 using SHELXL-2013 [6] using the program
X-Seed as a graphical interface [7]. Hydrogen atoms were
located in the difference maps but were placed in idealized
positions and refined with a riding model. Abbreviated
crystallographic details are collected in Table 1.
123

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J Chem Crystallogr (2015) 45:466–475
Table 1 Crystallographic data for complexes 1–4
1
2
3
4
Formula
C21H8BrF4N
1413645
430.18
C21H8BrF4N
1413647
430.18
C21H8IF4N
1413644
477.18
C21H10BrF2N
1413646
394.20
CCDC
Formula weight
Crystal dim. (mm3)
Crystal system
Space group
0.20 9 .20 9 .02
Triclinic
0.02 9 .20 9 .40
Triclinic
P-1
0.06 9 .24 9 .53
Triclinic
0.02 9 .20 9 .40
Monoclinic
P21/c
P-1
P-1
´
˚
a (A)
6.3332(4)
7.4288(4)
17.8897(10)
91.0980(10)
90.8580(10)
94.3830(10)
2
6.1324(13)
11.264(2)
13.064(3)
66.646(3)
89.736(3)
87.726(3)
2
6.1671(5)
11.2571(9)
13.3083(11)
66.2870(10)
88.1990(10)
87.3820(10)
2
18.7781(7)
3.83820(10)
22.9321(9)
90
´
˚
b (A)
´
˚
c (A)
a (°)
b (°)
c (°)
Z
102.6180(10)
90
4
´
3
˚
V (A )
838.95(8)
1.703
827.8(3)
1.726
844.94(12)
1.876
1612.89(10)
1.623
qcalcd (mg m-3
)
T (K)
l (mm-1
100
100
100
100
)
2.496
2.530
1.941
2.572
Reflections/unique
Data/restraints/parameters
Goodness of fit
10988/3687
3687/0/1244
1.045
9964/3608
3608/0/1244
1.065
10646/3730
3730/0/244
1.071
19674/3578
3578/0/226
1.059
R1/wR2
0.028/0.1065
0.033/0. 067
0.40/-0.41
0.035/0.095
0.040/0.099
1.44/-0.83
0. 027/0. 064
0.030/0. 066
0.86/-0.47
0.020/0.050
0.022/0.051
0.536/-0.23
R1/wR2 (all data)
3
Largest diff. peak/hole (eA )
˚
Fig. 1 Synthetic scheme for the synthesis of compound 1, 2-[[4-[(3-bromotetrafluorophenyl)ethynyl]phenyl]ethynyl]pyridine
terminal alkyne 6 in modest yield. Sonogashira coupling of
6 with 1,3-dibromotetrafluorobenzene yielded compound 1
in low overall yield. The reaction conditions and yields were
not optimized.
Results and Discussion
The compounds 1–4 were prepared using three successive
Sonogashira coupling reactions. The synthesis of compound
1 is outlined in Fig. 1. Initial coupling of 2-ethynylpyridine
with 1,4-diiodobenzene yielded 2-(4-iodophenylethynyl)
pyridine, 5. Subsequent reaction of 5 with trimethylsi-
lylethyne followed by base promoted deprotection yielded
Compounds 2, 3 and 4 were synthesized in a similar
manner starting from 3-ethynylpyridine as shown in Fig. 2.
All compounds were analyzed by a combination of 1H, 13
C
and 19F NMR spectroscopy and the chemical shifts and
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J Chem Crystallogr (2015) 45:466–475
471
Fig. 2 Synthetic scheme for the
synthesis of compounds 2–4
Fig. 3 View of the self-complementary halogen bonded dimer formed with 2-[[4-[(3-bromotetrafluorophenyl)ethynyl]phenyl]ethynyl]pyridine,
1, (a) along with an orthogonal view to emphasize slight twist of the molecule (b). Thermal ellipsoids drawn at the 50 % level
coupling constants of the halophenyl and pyridyl rings
were consistent with related compounds reported in our
earlier study [2].
are not however coplanar: the pyridyl ring is angled out of the
plane of the fluorophenyl ring with an angle of approximately
˚
151°. The NÁÁÁBr distance in 1 is 3.003(4) A which is 88 % of
˚
the sum of the van der Waals radii of 3.40 A. [10] This is
Compound 1 was recrystallized from chloroform as
needles. Self-complementary dimer formation in the solid
state was confirmed on X-ray analysis of the crystalline
solid. The dimeric unit of 1 is shown in Fig. 3.
˚
similar to the NÁÁÁBr distance of 3.029(2) A reported for
2-[(3-bromo-2,4,5,6-tetrafluorophenyl)ethynyl]pyridine [2].
The torsional angle between the pyridyl and phenyl rings is
approximately 6.5° and the torsional angle between the
central phenyl ring and the fluorophenyl ring is about 15°.
The aromatic rings twist in the same direction relative to the
The halogen bond is almost linear with a C–BrÁÁÁN angle
of 172.37(3)° in accord with n ? r* nature of the halogen
bonding interaction [8, 9]. The pyridyl and fluorophenyl rings
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J Chem Crystallogr (2015) 45:466–475
Fig. 4 View highlighting the weak intermolecular interactions, FÁÁÁF and C–HÁÁÁF, between halogen bonded dimers of 2-[[4-[(3-
bromotetrafluorophenyl)ethynyl]phenyl]ethynyl]pyridine, 1
Fig. 5 Three dimensional packing of the halogen bonded dimers of 2-[[4-[(3-bromotetrafluorophenyl)ethynyl]phenyl]ethynyl]pyridine, 1,
viewed along the b-axis
central phenyl ring as shown in Fig. 3b. There is a close FÁÁÁF
contact and a variety of weak C-HÁÁÁF interactions and p-
stacking that help stabilize the three-dimensional packing of
dimeric units. While the FÁÁÁF distance, F4ÁÁÁF4#1 denoted as
The dimer units are offset p-stacked with the central
phenyl ring and the halophenyl ring alternating in the
stacks (Fig. 5). The closest centroid to centroid distance
˚
between these rings is 3.67 A. with a closest atom to atom
˚
distance of about 3.5 A. The pyridyl rings have no close
˚
(b) in Fig. 4, of 2.889 A is only marginally less than the sum
˚
of the van der Waals radii of 2.94 A, the C-HÁÁÁF distances of
contacts.
˚
2.397, 2.511 and 2.601 A for F1ÁÁÁH11, F3ÁÁÁH14 and
The structures of compounds 2 and 3 are isostructural
with space group P-1 and Z = 2. Individual molecules of 2
and 3 are essentially planar with a distinct bent overall
shape as shown in Fig. 5. As expected two complementary
halogen bonds facilitate dimer formation. Both of the
halogen bonds are almost linear in both structures with a
C–BrÁÁÁN angle of 171.58(3)° and a C-IÁÁÁN angle of
F2ÁÁÁH19 are 89.8, 94 and 97.4 % of the sum of the van der
˚
Waals radii (2.67 A) respectively. These interactions are
labelled (c), (d) and (e) in Fig. 4. These C–HÁÁÁF distances
and angles compare favorably to those reported in the in-
depth study of weak phenyl C–HÁÁÁF interactions observed in
a series of polyfluorobenzenes reported by Thallandi et al. in
1998 [11].
˚
171.73(4)°. The NÁÁÁBr distance in 2 is 2.986(4) A, 85 % of
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J Chem Crystallogr (2015) 45:466–475
473
Fig. 6 View of the self-complementary halogen bonded dimer formed with 3-[[4-[(2-iodotetrafluorophenyl)ethynyl]phenyl]ethynyl]pyridine, 3,
(a) along with two orthogonal views to show the planarity of the molecule (b, c). Thermal ellipsoids drawn at the 50 % level
the sum of the van der Waals radii, while the NÁÁÁI distance
alkynyl carbons in 3 is 175.3° (see Fig. 6a angles C5–C6–
C7, C6–C7–C8, C11–C14–C15 and C14–C15–C16). It is
noteworthy that in the structure of compound 1 this bend is
not observed. This lack of bend in 1 is likely a consequence
of the internal fluorine atom (F1 in Fig. 3) which is
involved in supportive C–HÁÁÁF interactions on the interior
of the halogen-bonded dimer.
˚
in 3 is 2.905(6) A, 82 % of the sum of the van der Waals
radii, is slightly shorter in accord with the more intense
sigma hole on iodine as compared to bromine [12]. The
obvious bend of the molecules (Fig. 6a) is similar for
compound 2 and 3. For 2 the average angle around the
alkynyl carbons is 174.9° while the average angle about the
Fig. 7 View along (110) of a portion of the two-dimensional sheet comprising self-complementary dimers of 3 showing the unit cell with labels
and the four weak C–HÁÁÁF interactions (d, e, f and g)
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J Chem Crystallogr (2015) 45:466–475
Fig. 8 a View of the hydrogen bonded dimer formed with 3-[[4-[(2-bromo-4,5-difluorophenyl)ethynyl]phenyl]ethynyl]pyridine, 4, with the
asymmetric unit labeled and thermal ellipsoids drawn at the 50 % level. b Orthogonal view corresponding to a
Compounds 2 and 3 form two-dimensional sheets that
are p-stacked to form the three-dimensional structure. A
portion of the two-dimensional sheet formed from close
packed dimeric units of 3 is shown in Fig. 7.
The dimeric units of 3 are close packed with two pyridyl
C–HÁÁÁF interactions (d and e in Fig. 6) and two phenyl
C–HÁÁÁF interactions (f and g in Fig. 7) that serve to sta-
bilize the two-dimensional sheets. The distances F1ÁÁÁH3
Fig. 9 View of a one-dimensional sheet of the hydrogen bonded dimer formed with 3-[[4-[(2-bromo-4,5-difluorophenyl)ethynyl]phenyl]
ethynyl]pyridine 4
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J Chem Crystallogr (2015) 45:466–475
475
(d), F3ÁÁÁH4 (e), F3ÁÁÁH9 (f), and F4ÁÁÁH9 (g) are 2.458,
Supplementary Material
˚
2.674, 2.697 and 2.462 A respectively as compared to the
˚
sum of the van der Waals radii of 2.67 A which compare
CCDC 1413644-1413647 contain the supplementary crys-
tallographic data for this paper. These data can be obtained
free of charge from The Cambridge Crystallographic Data
Centre via www.ccdc.cam.ac.uk/data_request/cif.
favorably to those reported by Thallandi et al. [11].
In contrast to compounds 1–3 the difluoro compound 4,
3-(2-bromo-4,5-difluorophenylethynyl) pyridine, formed
twisted C–HÁÁÁN hydrogen bonded dimeric units interlinked
with a C–Br alkyne interaction as shown in Fig. 8. The
formation of a hydrogen bonded dimer was also observed
with the shorter difluoro analogue 3-[[2-bromo-4,5-difluo-
rophenyl]ethynyl]pyridine [2].
Acknowledgments We thank the National Science Foundation for
financial support of this research (RUI Grant No. 1306284) and the
Missouri State University Provost Incentive Fund that funded the
purchase of the X-ray diffractometer.
The non-conventional C–HÁÁÁN hydrogen bond has an
˚
NÁÁÁH distance of 2.426 A compared to the sum of the van
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˚
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