Competing hydrogen-bond and halogen-bond donors in crystal engineering

Article abstract of DOI:10.1039/c2ce26747k

In order to study the structure-directing competition between hydrogen- and halogen-bond donors we have synthesized two ligands, 3,3′-azobipyridine and 4,4′-azobipyridine, and co-crystallized them with a series of bi-functional donor molecules comprising

Full text of DOI:10.1039/c2ce26747k

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Competing hydrogen-bond and halogen-bond donors
in crystal engineering3
Cite this: CrystEngComm, 2013, 15,
125
3
Christer B. Aaker o¨ y,* Sheelu Panikkattu, Prashant D. Chopade and John Desper
In order to study the structure-directing competition between hydrogen- and halogen-bond donors we
have synthesized two ligands, 3,39-azobipyridine and 4,49-azobipyridine, and co-crystallized them with a
series of bi-functional donor molecules comprising an activated halogen-bond donor (I or Br) as well as a
hydrogen-bond donor (acid, phenol or oxime) on the same backbone. Based on the subsequent single-
crystal analysis, 5 of 6 co-crystals of 3,39-azobipyridine are assembled using hydrogen bonds as the primary
…
driving force accompanied by weaker secondary (C–X O) interactions. However, in 5 out of the 6 co-
…
…
crystals of 4,49-azobipyridine, both hydrogen bonds (O–H N) and halogen bonds (C–X N) are present as
structure-directing interactions leading to 1-D chains. Since the charges on the acceptor sites in 3,39- and
Received 23rd October 2012,
Accepted 27th November 2012
4
,49-azobipyridine are very similar, the observed difference in binding behaviour highlights the importance
of binding-site location on the acceptor molecules (anti-parallel in 3,39-azobipyridine and co-linear in
,49-azobipyridine) as a direct influence over the structural balance between hydrogen- and halogen-bond
DOI: 10.1039/c2ce26747k
4
www.rsc.org/crystengcomm
donors.
4
-bromotetrafluorophenol (OH-Br), 4-iodotetrafluoroaldoxime
Introduction
(Ox-I) and 4-bromotetrafluoroaldoxime (Ox-Br) (Scheme 1).
1
…
2
Many hydrogen-bond based synthons such as acid pyridine,
These probe molecules were subsequently co-crystallized with
two isomeric symmetric acceptors 3,39- and 4,49-azobipyridine
…
3
…
4
…
5
acid amide, phenol pyridine, oxime N(heterocycle) have
been explored extensively as robust and reliable tools for
crystal engineering and supramolecular synthesis. Recently,
(3,39-azpy and 4,49-azpy, respectively) (Scheme 1).
In this study, we investigate the following:
6
halogen bonds, which play important roles in areas such as
1) Competition between HB and XB donors for the pyridine
7
8
9
biochemistry, medicinal chemistry, and material science,
nitrogen atoms which are capable of forming both hydrogen
bonds and halogen bonds (Scheme 2).
have found uses in crystal engineering because these interac-
tions have properties that parallel those of hydrogen bonds in
terms of directionality and strength.
2) Possible influence of geometric differences of the donors
1
0,11
Typical hydrogen-
and acceptors on the competition and overall structural
outcome.
2
1 12
bond strengths range from approximately 4–60 kJ mol
,
2
1
while halogen bonds range from 5–180 kJ mol (the strong
3) Participation of auxiliary potential acceptors like
2…
2
I
3
2
13
interaction I
in I
is the extreme). Consequently,
carbonyl oxygen atoms, hydroxyl oxygen atoms and azo
nitrogen atoms (Scheme 3) in weaker interactions with
halogen atoms.
In Scheme 2, we have outlined the postulated structural
outcomes of the co-crystallizations as a function of the relative
strength and supramolecular efficiency of HB vs. XB in this
series of co-crystallizations.
iodine/bromine, suitably ‘activated’ through a fluorinated
backbone, should be capable of competing with hydrogen
bonds in a supramolecular reaction.
The combination of hydrogen bonds (HBs) and halogen
1
4
1
5
bonds (XBs) is gaining importance in crystal engineering,
and in order to investigate the structure-directing balance
between HBs and XBs we decided to employ a set of bi-
functional donor molecules equipped with one HB donor and
one XB donor attached to the same molecular backbone;
It is well known that electrostatic charge is important for
1
6
predicting or rationalizing molecular recognition events, but
in this study, the two acceptor molecules have rather similar
electrostatic potentials of interaction as indicated by the
4-iodotetrafluorobenzoic acid (COOH-I), 4-bromotetrafluoro-
2
1
benzoic acid (COOH-Br), 4-iodotetrafluorophenol (OH-I),
values of 2174 and 2172 kJ mol for 3,39-azpy and 4,49-azpy
respectively, corresponding to the minima in the molecular
electrostatic potential surface (0.002 e au ) determined using
a positive charge in vacuum as the probe after optimizing their
molecular geometries using DFT (B3LYP) with a 6-31++G**
basis set. There is therefore no real charge-based ‘bias’
Department of Chemistry, Kansas State University, Manhattan, KS, 66506, USA.
E-mail: aakeroy@ksu.edu
21
3
Electronic supplementary information (ESI) available: Details of the synthesis
of compounds. CCDC 906983–906994. For ESI and crystallographic data in CIF
or other electronic format see DOI: 10.1039/c2ce26747k
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Scheme 3 Potential secondary interactions between halogen atoms, X, and
suitable electron-pair donors.
Experimental set up
A library of six bifunctional halogen–hydrogen bond donors
and two symmetric acceptors (Scheme 1) was employed.
1
7
3
,39-Azobipyridine and 4,49-azobipyridine, 4-iodotetrafluor-
1
8
obenzoic acid and 4-bromotetrafluorobenzoic acid were
synthesised as reported. 4-Iodotetrafluorophenol was synthe-
sised from iodopentafluorobenzene using potassium hydro-
xide in tert-butanol (see ESI
-bromotetrafluoroaldoxime were synthesised in one-step
from their corresponding 4-halotetrafluoroaldehydes via a
3
). 4-Iodotetrafluoroaldoxime and
4
1
9
green solvent-assisted grinding method. Synthesis of all the
HB–XB donors is included in the ESI.
-Bromotetrafluorophenol was purchased from Sigma
Aldrich. The donors and acceptors were combined in
stoichiometric amounts giving total of 12 co-crystal
combinations, Table 1. Single crystals were obtained upon
slow evaporation of the solvent, and we were able to obtain
crystals suitable for single-crystal diffraction for products from
all twelve reactions.
3
4
a
Scheme 1 Bi-functional donors and isomeric symmetric acceptors.
between the two acceptors. However, there is a geometric
difference since the binding sites differ in their relative
orientation, i.e. in case of 3,39-azpy, the pyridine nitrogen
atoms are aligned anti-parallel whereas in 4,49-azpy they are
co-linear with respect to each other (Scheme 1). It is
conceivable that this difference may affect the primary
molecular recognition events, which can subsequently lead
to the formation of distinctly different supramolecular
assemblies.
X-Ray crystallography
Datasets were collected on a Bruker SMART APEX II system
with Mo radiation (3,39-azpy:COOH-I, 3,39-azpy:OH-I)
3,39-azpy:OH-Br,
3,39-azpy:Ox-I,
3,39-azpy:Ox-Br,
4,49-azpy:COOH-I, 4,49-azpy:OH-Br, 4,49-azpy:Ox-I or a Bruker
Kappa APEX II system with Cu radiation (3,39-azpy:COOH-Br,
4
,49-azpy:COOH-Br, 4,49-azpy:OH-I, 4,49-azpy:Ox-Br) at 120 K
2
0
using APEX2 software. An Oxford Cryostream 700 low-
temperature device was used to control temperature. Initial
cell constants were found by small widely separated ‘‘matrix’’
runs. Data collection strategies were determined using
COSMO. Scan speeds and scan widths were chosen based
on scattering power and peak rocking curves.
2
1
Unit-cell constants and orientation matrices were improved
by least-squares refinement of reflections threshold from the
2
2
entire dataset. Integrations were performed with SAINT,
using these improved unit cells as a starting point. Precise unit
cell constants were calculated in SAINT from the final merged
datasets. Lorenz and polarization corrections were applied.
2
3
Absorption corrections was applied using SADABS.
2
4
Datasets were reduced with SHELXTL. The structures were
solved by direct methods without incident. Coordinates for all
oxime and phenol hydrogen atoms were allowed to refine. All
other hydrogen atoms were assigned to idealized positions
and were allowed to ride. Isotropic thermal parameters for the
hydrogen atoms were constrained to be 1.56 (methyl)/1.26
(all other) that of the connected atom.
Scheme 2 Postulated outcomes.
3
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Table 1 Synthesis of 3,39- and 4,49-azobipyridine co-crystals
Acceptors
Donors
Co-crystal abbreviation
Mole ratio
Solvent/method
Melting points, uC
3
,39-Azobipyridine
4-Iodotetrafluorobenzoicacid
3,39-azpy:COOH-I
3,39-azpy:COOH-Br
3,39-azpy:OH-I
3,39-azpy:OH-Br
3,39-azpy:Ox-I
3,39-azpy:Ox-Br
4,49-azpy:COOH-I
4,49-azpy:COOH-Br
4,49-azpy:OH-I
4,49-azpy:OH-Br
4,49-azpy:Ox-I
1 : 1
1 : 1
1 : 1
1 : 1
1 : 1
1 : 1
1 : 1
1 : 1
1 : 1
1 : 1
1 : 1
1 : 1
Ethanol/slow evaporation
Ethanol/slow evaporation
Ethanol/slow evaporation
Ethanol/slow evaporation
Ethanol/slow evaporation
Ethanol/slow evaporation
Ethanol/slow evaporation
Ethanol/slow evaporation
Ethanol/slow evaporation
Ethanol/slow evaporation
Ethanol/slow evaporation
Ethanol/slow evaporation
182–185
155–157
125–127
170–173
145–148
105–108
220–222
190–191
163–165
133–136
115–116
125–126
4
4
4
4
4
-Bromotetrafluorobenzoicacid
-Iodotetrafluorophenol
-Bromotetrafluorophenol
-Iodotetrafluoroaldoxime
-Bromotetrafluoroaldoxime
4
,49-Azobipyridine
4-Iodotetrafluorobenzoicacid
4
4
4
4
4
-Bromotetrafluorobenzoicacid
-Iodotetrafluorophenol
-Bromotetrafluorophenol
-Iodotetrafluoroaldoxime
-Bromotetrafluoroaldoxime
4,49-azpy:Ox-Br
3
,39-azpy:COOH-I. Two orientations for the haloacid were
4,49-azpy:OH-I. The phenol hydrogen atom H31 was placed
in an idealized geometry and allowed to ride on its parent
oxygen atom.
located, in roughly head-to-tail positions. Geometry for the two
components was restrained to similarity by using the SHELXL
‘
‘SAME’’ command. Thermal parameters of closely located
4,49-azpy:OH-Br. Coordinates for the phenol hydrogen atom
H11 were allowed to refine.
4,49-azpy:Ox-I. Coordinates for the oxime hydrogen atom
H37 were allowed to refine.
atoms were pairwise constrained using the SHELXL ‘‘EADP’’
command. Coordinates of the ammonium hydrogen atom H11
were allowed to refine.
3
,39-azpy:COOH-Br. Coordinates for the carboxylic acid
hydrogen atom H21 were allowed to refine.
,39-azpy:OH-I. Coordinates for the carboxylic acid hydrogen
atom H21 were allowed to refine.
,39-azpy:OH-Br. Coordinates for the phenol hydrogen
atoms H31 and H41 were allowed to refine.
,39-azpy:Ox-I. Coordinates for the oxime hydrogen atom
H27 were allowed to refine.
,39-azpy:Ox-Br. Coordinates for the oxime hydrogen atom
H17 were allowed to refine
,49-azpy:COOH-I. The sample was a racemic twin, and
4,49-azpy:Ox-Br. Coordinates for the oxime hydrogen atom
H27 were allowed to refine.
Selected hydrogen and halogen-bond geometries are shown
in Tables 2 and 3 respectively. The crystallographic parameters
of 3,39- and 4,49-azobipyridine co-crystals are listed in Tables 4
and 5, respectively.
3
3
3
3
Results
Co-crystals of 3,39-azobipyridine
4
populations of the two components were parameterized using
the SHELXL ‘‘TWIN’’ and ‘‘BASF’’ commands. Two orienta-
tions for the haloacid were located, in roughly head-to-tail
positions. Geometry for the two components was restrained to
similarity by using the SHELXL ‘‘SAME’’ command. Thermal
parameters of closely located atoms were pairwise constrained
using the SHELXL ‘‘EADP’’ command. Thermal parameters for
the nearly inversion-related pyridines N11–C16 and N21–C26
were also constrained using the ‘‘EADP’’ command, and these
thermal parameters were restrained to approximately the same
values using the SHELXL ‘‘SIMU’’ command. The ammonium
hydrogen atom H11 was placed in an idealized geometry and
allowed to ride on its parent nitrogen atom.
3,39-Azobipyridine:4-iodotetrafluorobenzoic acid. The crys-
tal structure determination of 3,39-azpy:COOH-I shows that the
result is a neutral molecular solid with two acid molecules for
every one bipy. The co-crystal is formed via two symmetry
…
related O–H N hydrogen bonds between one carboxylic acid
and a nitrogen atom, Table 2. These interactions lead to
trimeric supermolecules which are subsequently connected
…
into 2-D corrugated sheets via C–I O(CLO) contacts (Fig. 1).
3,39-Azobipyridine:4-bromotetrafluorobenzoic acid. In the
3
,39-azpy:COOH-Br co-crystal, the primary driving force is a
…
pair of acid-pyridine O–H N hydrogen bonds which produce
neutral trimers that are further extended into 2-D sheets via C–
…
Br O
interactions (Fig. 2).
(CLO)
3,39-Azobipyridine:4-iodotetrafluorophenol.
4-
4,49-azpy:COOH-Br. The asymmetric unit contains two acid–
Iodotetrafluorophenol has two potential single point donors,
i.e. I and OH that could potentially bind to the nitrogen atoms.
In 3,39-azpy:OH-I however, hydroxyl hydrogen atom interacts
base pairs, each of which was assigned to a SHELXL RESI due
for consistent labelling purposes. Two orientations for each
halo acid were located, in roughly head-to-tail positions.
Similarly, two closely related orientations for the amine were
found. Geometry for all four acid components was restrained
to similarity by using the SHELXL ‘‘SAME’’ command.
Geometry for all four base components was also restrained
to similarity by using the SHELXL ‘‘SAME’’ command. Thermal
parameters of closely located atoms were pairwise constrained
using the SHELXL ‘‘EADP’’ command.
…
with the nitrogen atoms in symmetry related O–H N hydro-
gen bonds leading to a trimeric supermolecule. These trimers
are then further connected into 2-D sheets via weaker C–
…
I O
interactions (Fig. 3).
CLO)
(
3
,39-Azobipyridine:4-bromotetrafluorophenol.
In
the
…
3
,39-azpy:OH-Br co-crystal, intermolecular O–H N hydrogen
bonds direct the formation of primary trimeric building
blocks. The interaction of the bromine atom with a hydroxyl
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a
Table 2 Hydrogen-bond geometries in co-crystals of 3,39- and 4,49-azobipyridine
…
…
…
…
Compound
D–H A/Å
D–H/Å
H
A/Å
D
A/Å
D–H N/u
…
3
3
3
3
,39-azpy:COOH-I
,39-azpy:COOH-Br
,39-azpy:OH-I
N(11)–H(11) O(21A)_#1
1.22(2)
1.14(3)
0.90(2)
0.88(2)
0.88(2)
0.72(2)
0.76(4)
0.88
1.32(2)
1.41(3)
1.75(2)
1.77(2)
1.73(2)
2.18(2)
1.95(4)
1.75
1.73
1.76
1.84
1.75
1.83
1.84
1.86(2)
1.90(2)
1.79(6)
2.536(2)
2.549(2)
2.6162(15)
2.6224(16)
2.5963(15)
2.8460(17)
2.708(3)
2.605(9)
2.598(6)
2.566(10)
2.67(3)
2.587(9)
2.67(4)
2.614(4)
2.6342(16)
2.7052(19)
2.704(6)
174(2)
177(3)
159(2)
163.2(18)
166.8(18)
153(2)
178(4)
164.3
167.5
158.8
167.6
170.0
175.3
152.3
155(2)
169(2)
162(6)
…
O(21)–H(21) N(11)_#1
…
O(21)–H(21) N(11)_#1
…
,39-azpy:OH-Br
O(31)–H(31) N(11)
…
O(41)–H(41) N(21)
…
3
3
4
,39-azpy:Ox-I
,39-azpy:Ox-Br
,49-azpy:COOH-I
O(27)–H(27) N(27)_#1_#2
…
O(17)–H(17) N(21)_#1
…
N(11)–H(11) O(31B)_#1
0.88
…
…
…
…
4
,49-azpy:COOH-Br
O31A1–H31A1 N11A1
O31B1–H31B1 N21B1_#1
O31A2–H31A2 N11A2
0.84
0.84
0.84
0.84
O31B2–H31B2 N21B2_#2
…
4,49-azpy:OH-I
4,49-azpy:OH-Br
4,49-azpy:Ox-I
4,49-azpy:Ox-Br
O(31)–H(31) N(11)
0.84
…
O(31)–H(31) N(11)
0.83(2)
0.82(2)
0.94(6)
…
O(37)–H(37) N(11)
…
O(27)–H(27) N(11)_#1
a
Symmetry codes: 3,39-azpy:COOH-I #1 2x 2 1, 2y, 2z + 2. 3,39-azpy:COOH-Br #1 2x + 2, 2y + 1, 2z. 3,39-azpy:OH-I #1 2x + 1, 2y + 1, 2z +
. 3,39-azpy:Ox-I #1 2x, 2y, 2z + 2; #2 2x + 3, 2y + 1, 2z. 3,39-azpy:Ox-Br #1 2x, 2y, 2z 2 1. 4,49-azpy:COOH-I #1 x + 2, y 2 2, z + 1.
,49-azpy:COOH-Br #1 x 2 1, y + 1, z + 1; #2 x + 2, y + 1, z + 1. 4,49-azpy:Ox-Br #1 2x + 2, 2y + 3, 2z + 1.
1
4
…
oxygen lone pair links neighbouring trimers into 2-D
assemblies (Fig. 4).
with bromine in a C–Br O contact producing a 2-D layer
(Fig. 6).
3
,39-Azobipyridine:4-iodotetrafluoroaldoxime. In the co-crys-
Co-crystals of 4,49-azobipyridine
…
tal of 3,39-azpy:Ox-I, iodine atoms form C–I N halogen bonds
with the two pyridine nitrogen atoms, while the oxime
participates in a self-complementary dimer (Fig. 5). This
results in a 1-D non-planar corrugated chain-like assembly
with the donor and acceptor molecules aligned almost
perpendicular to each other. Among all the co-crystals of
,39-azobipyridine with bifunctional donor molecules, this is
the only example in which halogen bonds (not hydrogen
bonds) are present as the primary mode of interaction.
4,49-Azobipyridine:4-iodotetrafluorobenzoic acid. In the
…
4
,49-azpy:COOH-I co-crystal, intermolecular O–H N hydrogen
…
bonds and C–I N halogen bond interactions produce infinite
1
-D chain-like assemblies as the primary supramolecular
motifs (Fig. 7).
,49-Azobipyridine:4-bromotetrafluorobenzoic acid. The
4
3
4,49-azpy:COOH-Br co-crystal contains infinite 1-D chains
…
formed via intermolecular O–H N hydrogen bonds and
…
near-linear C–Br N halogen bonds (Fig. 8).
3,39-Azobipyridine:4-bromotetrafluoroaldoxime. The struc-
4,49-Azobipyridine:4-iodotetrafluorophenol.
In
the
ture of 3,39-azpy:Ox-Br shows aldoxime hydrogen atoms
interacting with pyridine via symmetry related O–H N
hydrogen bonds, while the aldoxime oxygen atom interacts
…
4,49-azpy:OH-I co-crystal, both the hydroxyl hydrogen atom
and the iodine atom bind to a pyridine nitrogen atom,
resulting in an infinite 1-D chain (Fig. 9).
a
Table 3 Halogen-bond geometries in co-crystals of 3,39- and 4,49-azobipyridine
…
…
…
Compound
C–X
A
X
A/Å
C–X A/u
…
3
3
3
3
,39-azpy:COOH-I
,39-azpy:COOH-Br
,39-azpy:OH-I
C–(24A)–I(1) O(22A)_#2
2.8694(13)
2.8792(17)
3.0913(10)
3.1138(11)
3.0750(10)
2.8279(12)
3.0557(19)
2.796(5)
2.802(7)
2.960(3)
2.9717(12)
2.8200(15)
3.395(4)
170.66(6)
172.23(7)
156.81(4)
156.32(5)
158.68(5)
174.75(4)
158.49(9)
173.4(3)
…
C–(24)–Br(1) O(22)_#2
…
C(24)–I(1) O(21)_#2
…
,39-azpy:OH-Br
C(34)–Br(1) O(31)_#1
…
C(44)–Br(2) O(41)_#2
…
3
3
4
4
4
4
4
4
,39-azpy:Ox-I
C(24)–I(1) N(11)
…
,39-azpy:Ox-Br
,49-azpy:COOH-I
,49-azpy:COOH-Br
,49-azpy:OH-I
,49-azpy:OH-Br
,49-azpy:Ox-I
C(14)–Br(1) O(17)_#1
…
C(34A)–I(1A) N(21)_#1
…
C(34A1)–Br(1A1) N(21A1)_#1
176.9(4)
…
C(34)–I(1) N(21)_#1
165.98(11)
165.95(5)
178.38(5)
171.94(17)
…
C(34)–Br(1) N(21)_#1
…
C(34)–I(1) N(21)_#1
…
,49-azpy:Ox-Br
C(24)–Br(1) N(14)_#1
a
Symmetry codes 3,39-azpy:COOH-I #2 x + 1, 2y + 1/2, z 2 1/2. 3,39-azpy:COOH-Br #2 x 2 1, 2y + 1/2, z + 1/2. 3,39-azpy:OH-I #2 2x + 1/2, y 2
/2, 2z + 3/2. 3,39-azpy:OH-Br #1 2x + 1, y 2 1/2, 2z + 1/2; #2 2x, y + 1/2, 2z + 3/2. 3,39-azpy:Ox-Br #1 x, y + 1, z + 1. 4,49-azpy:COOH-I #1 x 2
, y + 2, z 2 1. 4,49-azpy:COOH-Br #1 x 2 1, y + 1, z + 1. 4,49-azpy:OH-I #1 x 2 2, y + 1, z + 1. 4,49-azpy:OH-Br #1 x + 2, y 2 1, z 2 1.
,49-azpy:Ox-I #1 x 2 1/2, 2y 2 1/2, z + 1/2. 4,49-azpy:Ox-Br #1 x 2 1/2, 2y + 3/2, z 2 1/2.
1
2
4
3
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Table 4 Crystallographic parameters of 3,39-azobipyridine co-crystals
3,39-azpy:COOH-I 3,39-azpy:COOH-Br 3,39-azpy:OH-I
3,39-azpy:OH-Br
3,39-azpy:Ox-I
3,39-azpy:Ox-Br
Formula moiety
(C10
H
8
N
4
)
2
(C10
(C HBrF
10Br
730.18
H
8
N
4
)
(C10
H
8
N
4
)
(C10
(C HBrF
10Br
674.16
H
8
N
4
)
(C10
H
2
8
N
4
)
(C10
(C
8 4
H N )
(
C
C
24
7
HF
H
4
IO
)
N
2
7
4
O
2
F
)
2
(C HF
6
4
IO)
2
N
6
4
O)
2
(C
7
H
H
F
4
INO)
2
7
H
2
BrF
12Br
728.22
4 2
NO)
F N O
2 8 6 2
Empirical formula
Molecular weight
10
F
8
I
2
4
O
4
C
24
H
2
8
N
4
O
4
C
22
H
10
F
8
I
2
4
O
2
C
22
H
2
F
8
N
4
O
2
C
24
12
F
8
I
2
N
6
O
2
C
24
H
824.16
768.14
822.20
Color, habit
Crystal system
Space group, Z
Orange rod
Monoclinic
Orange plate
Monoclinic
Orange plate
Monoclinic
C2/c, 4
Orange prism
Monoclinic
P2 /c, 4
1
Orange prism
Triclinic
P ¯1 , 1
Orange plate
Triclinic
P ¯1 , 1
1
P2 /c, 2
P2
1
/c, 2
a, Å
b, Å
c, Å
a, u
b, u
c, u
4.9020(3)
21.4561(12)
12.1298(7)
90.00
100.151(2)
90.00
1255.82(13)
0.71073
2.606
4.8724(3)
22.0007(13)
11.6936(7)
90.00
101.336(3)
90.00
1229.06(13)
1.54178
5.151
19.0228(11)
16.8636(10)
7.2425(4)
90.00
93.198(2)
90.00
2319.7(2)
0.71073
2.806
18.2149(8)
16.4379(7)
7.4736(4)
90.00
99.631(2)
90.00
2206.17(18)
0.71073
3.774
5.6341(4)
10.4834(7)
11.5197(8)
75.365(2)
77.562(2)
80.975(2)
639.09(8)
0.71073
2.556
8.3500(8)
8.3646(8)
9.8996(10)
105.765(3)
103.151(3)
99.733(3)
628.00(11)
0.71073
3.325
3
Volume, Å
X-Ray wavelength
m, mm
2
1
Absorption corr
Trans min/max
Reflections Collected
Multi-scan
0.4893/0.8186
13 823
Multi-scan
0.5657/0.7531
7259
Multi-scan
Multi-scan
0.3602/0.4906
62 309
Multi-scan
0.4951 0.7161
15 760
Multi-scan
0.4159/0.8255
10 635
0.4671/0.8497
18 196
3957
Independent 4126
2158
7628
4637
3773
Observed
Threshold expression
3713
2046
.2s(I)
0.0261
0.0688
3666
6276
.2s(I)
0.0265
0.0699
4497
.2s(I)
0.0186
0.0444
3174
.2s(I)
0.0480
0.1288
.2s(I)
0.0207
0.0508
1.064
.2s(I)
0.0176
0.0463
1.021
R
wR
S
1
(observed)
(all)
2
1.084
0.998
1.085
1.052
4
,49-Azobipyridine:4-bromotetrafluorophenol.
The
4,49-Azobipyridine:4-bromotetrafluoroaldoxime. Unlike in
the previous structures, in the 4,49-azpy:Ox-Br structure, the
aldoxime hydrogen atoms form oxime pyridine hydrogen
4
,49-azpy:OH-Br co-crystal displays 1-D infinite chains formed
via intermolecular O–H N hydrogen bonds and C–Br N
…
…
…
halogen bonds (Fig. 10).
bonds on both sides of the acceptor, while bromine on the
…
other end interacts with the azo nitrogen (C–Br N(azo),
4,49-Azobipyridine:4-iodotetrafluoroaldoxime.
In
the
4
,49-azpy:Ox-I co-crystal, 1-D infinite zig-zag chains are
3.397 Å) (Fig. 12). The bond distance is longer than a typical
C–Br Naromatic halogen bond (Aver. 3.04 Å), but slightly
…
…
…
constructed via hydrogen (O–H N) and halogen (C–I N)
bonds (Fig. 11).
shorter than the sum of their (Br and N) van der Waals radii
Table 5 Crystallographic parameters of 4,49-azobipyridine co-crystals
4,49-azpy:COOH-I
4,49-azpy:COOH-Br 4,49-azpy:OH-I 4,49-azpy:OH-Br
4,49-azpy:Ox-I
4,49-azpy:Ox-Br
Formula moiety
(C10
H
8
N
4
)
2
(C10
(C HBrF
BrF
457.19
Orange prism
Triclinic
P ¯1 , 4
H
8
N
4
)
(C10
H
8
N
4
)
(C10
(C HBrF
BrF
429.18
Colourless plate Orange plate
H
8
N
4
)
(C10
H
2
8
N
4
)
(C10
8 4
H N )
(
C
C
17
7
HF
H
4
IO
)
4
7
4
O
2
)
(C HF
6
4
IO)
IN
6
4
O)
(C
7
H
H
F
4
INO)
IN
(C
7
H
H
2
BrF
12Br
728.22
4 2
NO)
Empirical formula
Molecular weight
Color, habit
Crystal system
9
F
4
IN
O
2
C
17
H
9
4
N
4
O
2
C
16
H
9
F
4
4
O
C
16
H
9
4
N
4
O
C
17
10
F
4
5
O
C
24
2 8 6 2
F N O
504.18
476.17
Orange plate
Triclinic
P ¯1 , 2
503.20
Bronze plate
Triclinic
P1, 1
Orange needle
Monoclinic
P2 /n, 2
1
Triclinic
Monoclinic
C2/c, 8
Space group, Z
P ¯1 , 2
a, Å
b, Å
c, Å
a, u
b, u
c, u
6.2112(8)
8.1879(11)
8.9824(12)
84.843(3)
70.837(3)
77.402(3)
421.03(10)
0.71073
10.1607(5)
13.4553(6)
14.4474(8)
112.158(3)
90.592(3)
111.504(3)
1676.48(14)
1.54178
3.967
6.1515(5)
9.8197(7)
13.7443(10)
81.558(3)
85.932(3)
78.342(3)
803.57(10)
1.54178
16.211
6.3706(3)
9.5670(5)
13.3289(7)
79.453(2)
83.090(2)
79.4760(10)
782.03(7)
0.71073
2.687
17.6282(7)
6.3167(3)
31.7318(14)
90.00
96.518(2)
90.00
3510.6(3)
0.71073
1.884
10.2846(10)
4.6215(5)
27.841(2)
90.00
98.246(6)
90.00
1309.6(2)
1.54178
4.795
3
Volume, Å
X-Ray wavelength
m, mm
2
1
1.967
Absorption corr
Trans min/max
Multi-scan
0.5544/0.9255
8655
Multi-scan
0.5354/0.7420
18 301
Multi-scan
0.1813/0.5633
11 713
Multi-scan
0.5804/0.7464
17 166
Multi-scan
0.6401/0.9284
27 187
Multi-scan
0.5662/0.7531
7830
Reflections
Collected
5840
5035
.2s(I)
0.0851
0.2211
1.038
2764
2604
.2s(I)
0.0275
0.0756
1.082
5315
4829
.2s(I)
0.0269
0.0720
1.037
6206
5308
.2s(I)
0.0239
0.0575
1.040
2257
1721
.2s(I)
0.0595
0.1586
1.099
R
wR
S
1
2
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…
…
O(CLO) interactions in the 3,39-azpy:COOH-I co-crystal. The apparent ‘covalent’ bond between
Fig. 1 2-D network formed via strong O–H
N
(py) and weaker C–I
COOH and py is due to a disorder over two positions of the haloacid.
…
…
Fig. 2 3,39-azpy:COOH-Br co-crystal showing primary O–H
N
(py) and secondary C–Br
O(CLO) interactions.
…
…
O(CLO) interactions forming an eight component repeat unit.
Fig. 3 3,39-azpy:OH-I crystal structure showing primary O–H
N(py) and secondary C–I
… …
N(py) and C–Br O interactions forming the multi-component supermolecule.
Fig. 4 3,39-azpy:OH-Br crystal structure showing intermolecular O–H
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…
N(py) halogen bonds forming 1-D non-planar corrugated chain.
Fig. 5 3,39-azpy:Ox-I co-crystal with oxime–oxime dimer and C–I
…
…
Fig. 6 3,39-azpy:Ox-Br crystal structure showing O–H
N(py) primary hydrogen bonds and secondary C–Br O interactions.
…
…
N(py) hydrogen and halogen bond, respectively. For specific information
Fig. 7 1-D infinite chain in 4,49-azpy:COOH-I co-crystal formed via O–H
N
(py) and C–I
about the crystallography, see the Experimental section.
…
…
N(py) halogen-bond interactions.
Fig. 8 4,49-azpy:COOH-Br co-crystal showing primary O–H
N
(py) hydrogen bonds and C–Br
(
3.40 Å). Although there are very few examples of the halogen-
bi-functional donors comprising both a HB donor (acid,
phenol and oxime) as well as an XB donor (iodine and
bromine) on the same backbone. Single-crystal structural data
were acquired for solids obtained from all 12 reactions. The
primary interactions driving the crystal assembly were the O–
…
bonding ability of azo-nitrogen atoms this Br N(azo) interac-
tion aligns the azobipyridine almost perpendicular to the
plane, leading to a 3-D architecture, Fig. 13.
…
…
H N hydrogen bonds or C–X N halogen bonds followed
(
py)
(py)
by secondary interactions which were used to connect the
primary motifs. In all co-crystals, there were several potential
acceptors e.g. N(py), N(azo), O(–OLC) and O(–OH), and donors
e.g. acid, phenol, oxime, iodine and bromine. Considering the
Discussion
Twelve co-crystallizations were performed using two isomeric
pyridine-based acceptors (3,39- and 4,49-azobipyridine) and six
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…
…
N(py) interactions.
Fig. 9 4,49-azpy:OH-I crystal structure with 1-D chains formed via both O–H
N(py) and C–I
…
…
N(py)) bonds.
Fig. 10 The 4,49-azpy:OH-Br co-crystal contains 1-D chains formed by both hydrogen (O–H
N
(py)) and halogen (C–Br
…
…
N(py) interactions forming a 1-D chain.
Fig. 11 Part of the crystal structure of 4,49-azpy:Ox-I with C–I
N
(py) and O–H
…
…
N(azo) interactions.
Fig. 12 Part of the 4,49-azpy:Ox-Br crystal structure with O–H
N(py) hydrogen bonds and C–Br
complexity of such a system, and although it was reasonable to
expect some degree of structural ‘chaos’ in the supramolecular
outcome, we observe remarkable consistency in the binding
pattern within the two classes of acceptors. Table 6 and
Scheme 4 summarize the structural landscape in these twelve
crystal structures.
intermolecular bond distances. The search in CSD was limited
to aromatics alone. The average O N bond distances reported
…
for acid–pyridine (381 hits), phenol–pyridine (435 hits) and
aldoxime–pyridine (7 hits) are 2.63 Å, 2.74 Å and 2.71 Å
respectively; while for our crystal structures the corresponding
values are 2.60 Å, 2.62 Å and 2.71 Å. Based on the values
…
Data from the Cambridge Structural Database (CSD) were
obtained from CSD, the O N bond distance decreases in the
…
…
used to compare both O N as well as X N (X = I/Br)
following order, phenol–pyridine . oxime–pyridine . acid–
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…
nitrogen in 4/6 cases, whereas bromine forms C–Br N(py)
halogen bond in only 2/6 instances. Bromine interacts more
frequently with less basic secondary acceptors, i.e. ‘O’ and
‘Nazo’ 4/6 times, whereas iodine does so only 2/6 times.
Five of the six 3,39-azobipyridine co-crystals exhibit
…
OH N(py) interactions involving the best acceptor leading to
supramolecular trimers. The trimers are then linked into 2-D
corrugated sheets via weaker interactions between I/Br with a
secondary acceptor such as an oxygen atom. Thus, in this
group of structures, hydrogen bonds dominate over halogen
bonds, i.e. HB . XB (5/6) (Scheme 4). An outlier in this series is
3,39-azpy:Ox-I, where the XB donor interacts preferentially with
the N(py) acceptor. As a result, the ‘free’ oxime moiety forms a
dimer with an oxime from a neighbouring molecule leading to
2
5
infinite 1-D chain-like structure.
In contrast, in five out of six 4,49-azobipyridine co-crystals
Fig. 13 3D-architecture in the 4,4-9azpy:Ox-Br co-crystal.
1
-D chains are obtained via simultaneous O–H N(py) hydrogen
…
…
bonds and C–X N(py) (X = I/Br) halogen bonds. In this group,
both donors seem to be of equal importance in the primary
assembly process, i.e. HB $ XB (5/6) (Scheme 4). There is no
distinction between bromine and iodine as a halogen-bond
donor in any of the co-crystals. The only outlier in the series is
4,49-azpy:Ox-Br where oxime pyridine hydrogen bonds drive
the formation of the co-crystal i.e. HB . XB (1/6) (Scheme 4). It
is interesting to note the appearance of an unusual C–
Br N(azo) halogen bond in this structure. This observation
does introduce the possibility for a new prospective acceptor
site (azo nitrogen) that could be further explored in new
strategies for directed assembly of complex supramolecular
architectures.
Our results, which show a close competition between XB
and HB donors are consistent with the work of Resnati and co-
workers who designed a competitive experiment by combining
1,2-bis(4-pyridyl)-ethane (BPE) as a symmetric acceptor, 1,4-
diiodotetrafluorobenzene (DITFB) as halogen-bond donor and
pyridine. However our study shows the following trend, oxime–
pyridine . phenol–pyridine . acid–pyridine. The discrepancy
observed in the order between oxime and phenol could be due
to the limited number of crystal structure data (7 hits)
available for an oxime–pyridine interaction in the database.
It should be noted that it may not be possible to draw direct
inferences about intermolecular bond ‘strength’ based upon
…
…
…
observed D A distances due to the fact that many other
extraneous factors also contribute to the final molecular
arrangement within a crystalline solid. Nevertheless, the N O
distances observed in our co-crystals are within the range of
what is expected based upon information from the published
literature.
…
…
A similar search on aromatic halogen pyridine bond
…
…
distances provides average C–I N and C–Br N values of
.88 Å and 3.04 Å respectively. Based on our crystal structures,
2
2
6
…
…
the average C–I N and C–Br N bond distances are 2.86 Å and
…
hydroquinone (HQ) as hydrogen-bond donor in a single-pot.
2.90 Å respectively. These distances correspond to an N X
Selective halogen-bonded co-crystal formation was observed,
leaving the hydrogen-bond donor in a solution. The result
suggests suitable XB donors can compete with certain HB
donors and preferentially bind to the acceptor to give stable
binary co-crystals. These results complement work by Cho
et al. and Bruce et al. who designed liquid crystals using a
combination of both halogen as well as hydrogen bonds
affixed on the same backbone.
contraction of 18.3% and 10.6% compared to the combined
…
…
van der Waals radii of C I and C Br, respectively, which
demonstrates that the iodine atom is a significantly better
halogen-bond donor than the bromine atom (as long as both
are ‘activated’ to the same extent). This is also in good
agreement with the electrostatic argument which shows that
the s-hole on the iodine atom carries a higher positive charge
than that on the bromine atom. Moreover, iodine atoms form
2
7
28
There is a clear distinction between the primary molecular
recognition events in the two classes of azobipyridine co-
…
C–I N primary halogen bonds with the most basic pyridine
(
py)
a
Table 6 Summary of the main structural features in 3,39- and 4,49-azobipyridine co-crystals of dicarboxylic acids
COOH-I (acid-H)
COOH-Br (acid-H)
OH-I (phenol-H)
OH-Br (phenol-H)
Ox-Br (oxime-H)
Ox-I (oxime-H)
3
,39-azpy
,49-azpy
OH . I
A
OH = I
B
OH . Br
A
OH = Br
B
OH . I
A
OH = I
B
OH . Br
A
OH = Br
B
OHox . Br
A
OHox . Br
A
OHox , I
C
OHox = I
B
4
a
A: HB . XB, B: HB $ XB, C: HB , XB.
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crystals with same co-formers. In one case, hydrogen bonding
is the preferred interaction whereas in the other case HB and
XB seem to be of equal importance. This difference cannot be
explained on the basis of an electrostatically-based argument
on the acceptor molecules, since the charges on the nitrogen
atoms in the two azobipyridines differ only by a couple of kJ
mol . In order to seek a plausible explanation for the
difference in binding behaviour we examined the electrostatic
potentials of donor molecules as well as packing coefficients
and melting point trends in the two classes of co-crystals.
range of the other five structures, and the structural outlier in
the second family, 4,49-azpy:Ox-Br, is similarly unremarkable
in this context. Furthermore, as neither family (nor associated
outlier) displayed any exceptional melting points, it is unlikely
that a deeper analysis of weaker interactions or packing modes
can explain the general differences in molecular recognition
events that dominate in the two groups of co-crystals.
2
1
Since theoretical calculations, packing coefficients and
melting points could not be used to explain the differences
3
0
in binding events, this ‘synthon crossover’,
could be
rationalized based on the difference in binding site orienta-
tion in the two azobipyridine molecules.
Electrostatic surface potential calculations
The nitrogen atoms on 3,39-azobipyridine have an anti-
parallel orientation with respect to each other (Scheme 1). This
geometry does not favour the ready formation of 1-D chains as
the lack of ideal complementary means that adjacent
molecules need to be forcefully brought in close proximity at
angles that can enforce a 1-D assembly formation. In doing so
the overall energy of the system may increase while its stability
is compromised. On the other hand, forming discrete trimers
is less challenging and requires no considerable effort. These
trimers can be readily connected via secondary interactions
thus leading to a stable structure. Under these conditions, the
HB donor (which is a somewhat more competitive donor
moiety) binds to the best acceptor site, i.e. the pyridine
nitrogen, leading to a stable trimer. I/Br then interacts with the
next best acceptor (oxygen/azo nitrogen) linking the trimers
into a 2-D architecture.
Geometry optimizations were carried out and molecular
electrostatic potential surfaces, MEPS were evaluated on six
bi-functional donor molecules using Spartan, 2010 (Wave
function, Inc. Irvine, CA). Calculations were done using both
semi-empirical (PM3) and DFT methods (B3LYP, 6-31++G**
basis set). Table 7 summarizes the outcome of theoretical
calculations.
Despite numerical differences, both methods produced the
same trends with regards to the decreasing charge on the
acidic hydrogen atom on the three HB donor moieties
according to the following; phenol . acid . aldoxime. These
values also accurately reflect hydrogen-bond parameters for
2
9
common functional groups reported previously. As expected,
both methods also show larger positive values for the potential
surface of the s-hole on iodine compared to that on bromine.
Unfortunately, the MEPS values do not offer any additional
insight as to why co-crystals of 3,3-azpy are constructed mostly
through hydrogen-bonds whereas the 4,49-azpy co-crystals are
synthesized through a simultaneous use of both XB and HB
interactions.
In 4,49-azobipyridine however, the binding sites are co-linear
which naturally favours the formation of infinite 1-D chains
with no significant loss in energy. Under these conditions, the
acceptor nitrogen atom binds to an XB donor as quickly as it
binds to HB donor producing 1-D infinite chains constructed
Packing coefficients and melting points
…
…
form alternative D–H A and X A interactions. The take home
message from this analysis is that thermodynamically
favoured supramolecular assemblies (the 3,39-azpy co-crystals)
have time to maximize intermolecular interactions and there-
fore the HB donors ‘win’ over the XB donors. However, the
facile and rapid formation of more linear 1-D chains in the
4,49-azpy co-crystals represent kinetic products and in this case
there is a 50 : 50 chance that each bipy will be connected to an
XB and HB donor simultaneously which is what is observed in
five of the six co-crystals.
Packing coefficients were calculated for all 12 co-crystals using
the Olex2 v1.2 software, Tables 8 and 9.
The packing coefficients for the two classes of co-crystals
range from 66–74% and they show very similar values with the
same donor molecule. The structural outlier in the first family,
3,39-azpy:Ox-I, has a packing coefficient that is well within the
We have established that the orientation of the binding site
in the acceptor can influence supramolecular assembly in very
specific ways, and several points can be made based on the
crystal structure analysis for 3,39- and 4,49-azobipyridine co-
crystals:
1) In 3,39-azpy co-crystals hydrogen bonding is the primary
driving force (HB . XB), while in 4,49-azpy co-crystals both
2
1
Table 7 Electrostatic surface potentials expressed as charges in kJ mol
COOH-I COOH-Br OH-I
Br
PM3 144 222 144 160 156 202 163 152 134 204 135 147
DFT 296 166 305 142 305 155 314 121 283 153 276 129
OH-Br
Br
Ox-I
Ox-Br
Br
H
I
H
H
I
H
H
I
H
Scheme 4 Overview of the structural landscape 3,39- and 4,49-azobipyridine co-
crystals.
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Table 8 Packing efficiency and mp of 3,39-azpy co-crystals
COOH-I
COOH-Br
OH-I
OH-Br
Ox-I
Ox-Br
Packing coefficient (%)
Melting points (uC)
74
182–185
69
155–157
68
125–127
71
170–173
69
145–148
69
105–108
Table 9 Packing efficiency and mp of 4,49-azpy co-crystals
COOH-I
COOH-Br
OH-I
OH-Br
Ox-I
Ox-Br
Packing coefficient (%)
Melting points (uC)
74
220–222
76
190–191
67
163–165
69
133–136
66
115–116
67
125–126
hydrogen as well as halogen bonds equally contribute in the
assembly process (HB $ XB).
2004, 4, 89–94; (d) C. B. Aaker o¨ y, A. M. Beatty, B. A. Helfrich
and M. Nieuwenhuyzen, Cryst. Growth Des., 2003, 3,
159–165.
2
) Among the halogen atoms, iodine is a better halogen-
bond donor than bromine.
) There is no distinction between three types of hydrogen-
4
(a) K. S. Huang, D. Britton, M. C. Etter and S. R. Byrn, J.
Mater. Chem., 1997, 7, 713; (b) L. R. MacGillivray, J. L. Reid
and J. A. Ripmeester, J. Am. Chem. Soc., 2000, 122, 7817; (c)
T. Fri ˇs ˇc i ´c and L. R. McGillivray, Chem. Commun., 2009,
3
bond donors (–COOH, –OH and –CN(R)OH) in terms of
binding to the azobipyridines in the presence of halogens.
It is clear that more work is needed to tease out the precise
reason behind the observed patterns of behavior in these two
ditopic acceptors, and we have therefore embarked on a study
of comparable symmetric ditopic N-acceptors that offer the
same type of geometric differences that 3,39- and 4,49-azop
display. The fact that HB and XB strengths are comparable
773–775; (d) I. D. H. Oswald, W. D. S. Motherwell and
S. Parsons, Acta Crystallogr., 2004, 60, 1967–1969; (e) P.
S. Wheatley, A. J. Lough, G. Ferguson and C. Glidewell, Acta
Crystallogr., 1999, 55, 1489–1492; (f) A. Mukherjee and G.
R. Desiraju, Chem. Commun., 2011, 47, 4090–4092.
C. B. Aaker o¨ y, D. J. Salmon, M. M. Smith and J. Desper,
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