Towards a monomeric structure of phenylboronic acid: The influence of ortho-alkoxy substituents on the crystal structure

Article abstract of DOI:10.1039/c2ce25657f

The structures of three ortho-alkoxyphenylboronic acids (2-methoxy-, 2-ethoxy-, 2-isobutoxy-), and three diortho-alkoxyphenylboronic acids (2,6-dimethoxy-, 2,6-diethoxy- and 2-isobutoxy-6-methoxy) were determined by single crystal X-ray diffraction. The study was undertaken with the intention of designing a novel boronic acid having a monomeric structure, which to date has been an unavailable building block for crystal engineering. This motif can be enhanced by involving two hydroxyl groups at the boron atom in intramolecular hydrogen bonds. Although monosubstituted systems form typical dimers in the crystal lattice, disubstituted species reveal a much bigger variety of possible interactions. Among the analyzed compounds, 2,6-dimethoxyphenylboronic acid and 2,6-diethoxyphenylboronic acid crystallize in two polymorphic forms each. The unprecedented packing with monomers as the dominant structural motif has been found in the crystal structure of 2-isobutoxy-6-methoxyphenylboronic acid and one of the polymorphs of both 2,6-dimethoxyphenylboronic acid and 2,6-diethoxyphenylboronic acid. This description of the molecular packing is also supported by the analysis of fingerprint 2-D plots based on the Hirshfeld surfaces. The variety of possible types of interactions either within a single moiety or between moieties in dimers were additionally analyzed on the basis of the interaction energies, which have been estimated by ab initio calculations at the MP2/6-31+G* and B3LYP/6-311+G** level of theory.

Full text of DOI:10.1039/c2ce25657f

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PAPER
Towards a monomeric structure of phenylboronic acid: The influence of ortho-
alkoxy substituents on the crystal structure{
a
a
b
b
b
Michał K. Cyra n´ ski,* Paulina Klimentowska, Agata Rydzewska,{ Janusz Serwatowski, Andrzej Sporzy n´ ski
and Dorota K. St e˛ pie n´
a
Received 28th April 2012, Accepted 13th June 2012
DOI: 10.1039/c2ce25657f
The structures of three ortho-alkoxyphenylboronic acids (2-methoxy-, 2-ethoxy-, 2-isobutoxy-), and
three diortho-alkoxyphenylboronic acids (2,6-dimethoxy-, 2,6-diethoxy- and 2-isobutoxy-6-methoxy)
were determined by single crystal X-ray diffraction. The study was undertaken with the intention of
designing a novel boronic acid having a monomeric structure, which to date has been an unavailable
building block for crystal engineering. This motif can be enhanced by involving two hydroxyl groups
at the boron atom in intramolecular hydrogen bonds. Although monosubstituted systems form
typical dimers in the crystal lattice, disubstituted species reveal a much bigger variety of possible
interactions. Among the analyzed compounds, 2,6-dimethoxyphenylboronic acid and 2,6-
diethoxyphenylboronic acid crystallize in two polymorphic forms each. The unprecedented packing
with monomers as the dominant structural motif has been found in the crystal structure of
2
-isobutoxy-6-methoxyphenylboronic acid and one of the polymorphs of both 2,6-
dimethoxyphenylboronic acid and 2,6-diethoxyphenylboronic acid. This description of the molecular
packing is also supported by the analysis of fingerprint 2-D plots based on the Hirshfeld surfaces. The
variety of possible types of interactions either within a single moiety or between moieties in dimers
were additionally analyzed on the basis of the interaction energies, which have been estimated by ab
initio calculations at the MP2/6-31+G* and B3LYP/6-311+G** level of theory.
Introduction
bonds – e.g. covalent organic frameworks (COF), an emerging
class of crystalline, porous materials composed of organic
7,8
For many years crystal engineering has been an extremely fast
growing area of experimental chemistry leading to new materials
with a controlled and understood nature. Design and under-
standing the crystal architecture still remains challenging, as this
knowledge and experience impacts on the standard of life for
6
subunits, as well as by hydrogen bonds.
To date there are about 150 known diverse phenylboronic acid
9
structures. Five main factors play a crucial role in determining
the crystal architecture: (i) the electron-deficiency of the boron
10
center enabling dative bond formation, (ii) the flexibility of the
4,11
1
,2
each of us.
Phenylboronic acids are one of the class of
boronic group,
(iii) the presence of two hydroxyl groups in
12–14
molecular systems which have recently stimulated much interest,
not only due to the Suzuki coupling reaction in organic
different conformations (syn,syn, syn,anti or anti,anti),
(iv)
functional groups in the phenyl ring and last but not least (v) the
5–18
3
chemistry, but also due to their wide applications in catalysis,
1
presence of other components.
In addition to strong
4
medicine and biology. Great interest has been also paid to the
5
intermolecular hydrogen bonds in typical dimeric units and
1
supramolecular systems which can be formed by both covalent
1,19
lateral hydrogen bonds connecting them,
there are many
a
examples of weaker inter- and intramolecular bond formation
Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw,
Poland. E-mail: chamis@chem.uw.edu.pl; Fax: +48 22 8222892;
Tel: +48 22 8220211 ext. 360
Faculty of Chemistry, Warsaw University of Technology, Noakowskiego
determining the crystal architecture. Boronic acids are used as
20
tools for self assembly in supramolecular chemistry, but one of
b
the building blocks has never been taken into account. This
missing link is the monomer.
3, 00-664 Warsaw, Poland
Electronic supplementary information (ESI) available. It contains a full
{
list of bond lengths, bond angles and torsion angles of the experimentally
studied systems (1)–(6). It also contains symmetry, absolute electronic
energy at MP2/6231+G* and B3LYP/62311+G** (in Hartree) and
Cartesian coordinates at MP2/6231+G* and B3LYP/62311+G** levels
for the molecules studied. The detailed data relating to hydrogen bond
energies estimated at two levels of theory (MP2/6231+G* and B3LYP/
The architecture of phenylboronic acids is often compared
4,11
with that of benzoic acids.
In the latter, breaking of the dimer
motif is possible due to substitution in the ortho position by a
group enabling intramolecular hydrogen bond formation. This
21,22
can be done efficiently with the ethoxy substituent,
2
but
62311+G**) is also presented. See DOI: 10.1039/c2ce25657f
2,23
surprisingly not with methoxy.
This simple, albeit nice idea
{ Present address: Faculty of Chemistry, Wrocław University of
Technology, Wybrze z˙ e Wyspia n´ skiego 27, 50-370 Wrocław, Poland.
inspired us to devise monomeric structures of phenylboronic
6
282 | CrystEngComm, 2012, 14, 6282–6294
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acids. Support for this work comes from a survey of crystal
9
structures of mono ortho-substituted phenylboronic acids. The
2
4
25
vast majority of them, except fluoro-,
trifluoromethyl-
2
6
27
acetylphenyl- or 2-methoxycarbonyl- substituents, form an
intramolecular hydrogen bond involving the hydroxyl group at
boron and heteroatom(s) situated in the ortho position or in a
side chain. To obtain a monomeric motif, two hydroxyl groups
should be involved in intramolecular hydrogen bonds. In the
crystal field they should be strong enough to overcome
intermolecular hydrogen bond interactions. Obviously this may
be achieved if the boronic group is coplanar with the phenyl
fragment. In mono ortho-substituted systems this can be most
2
8,29
effectively achieved for alkoxy-
and for phenylazo-substitu-
3
0
ents. Importantly, the twist between the fragments is signifi-
Scheme 1 Structures of investigated compounds.
3
1
cantly smaller in the former case, which make them very
attractive.
groups (see Fig. 1). The group is always planar and almost
coplanar with the phenyl ring fragment with only a slight twist of
The aim of this paper is to devise a monomer structure by
systematic investigation of the influence of two ortho alkoxy
groups in phenylboronic acid on their molecular and crystal
structures. Comparison with reference systems containing one
ortho alkoxy group and estimation of the hydrogen bond
energies of the most common interactions observed in the crystal
lattice is another goal of this paper. The experimentally
investigated compounds are shown in Scheme 1.
4.11u (1), 7.41u (2) and 1.44u or 2.81u [two symmetrically
independent molecules of (3)].
The hydrogen bonds in the dimers are rather strong with the
…
˚
O12–H12 O11 distance in the range of 1.92(2)–1.96(2) A
…
˚
O11 O12 is in the range of 2.752(1)–2.840(2) A], see Table 1.
[
This is comparable with the distances in other phenylboronic
acids with polyoxaalkyl substituents at the ortho-position having
2
been studied before, but slightly longer than in the unsub-
9
Results and discussion
…
stituted phenylboronic acid (O
1
O
equals to 2.721 or
9,41
˚
.734 A).
2
Due to the presence of the alkoxy group ortho to
Structures
the boronic group, the hydroxyl group in the anti conformation
plays not only the role of hydrogen bond acceptor, but is also an
intramolecular hydrogen bond donor to the proximal oxygen
Structural details for all the obtained systems are given in Tables
4
and 5 (later), whereas the plots representing thermal
displacement ellipsoids together with the numbering scheme
are collected in Fig. 11 (later).
…
atom. The intramolecular O–H O bonds are somewhat shorter
˚
than the intermolecular ones and vary from 1.89(2) –1.94(2) A
…
˚
O distances in the range of 2.622(2) –2.664(1) A), which
(
O
A. 2-Alkoxyphenylboronic acids. The molecules of 2-methox-
yphenylboronic acid (1), 2-ethoxyphenylboronic acid (2) and
might suggest that they are stronger. In fact the estimations of
interaction energies do not support this view (see discussion
below).
2
-isobutoxyphenylboronic acid (3) crystallize in a monoclinic
system, with one molecule (1 and 2) or with two molecules (3) as
the asymmetric part of the unit cell. In all three structures
molecules form dimers, the most common motif observed in the
The dimers interact in the crystal lattice with other units by
…
weak intermolecular interactions. In (1) C–H O interactions
…
˚
O distance of 2.687(2) A) form infinite ribbons parallel to
(
H
9
,11
structures of phenylboronic acids.
These dimers are either
¯
the (141) plane (Fig. 2a). These ribbons are further zipped by
p
weak C –H O and C–H C interactions, while the layers of
…
…
p
centrosymmetric ((1), (2)) or asymmetric – i.e. formed by two
independent molecules (3). The boronic group in all cases shows
a similar geometry with syn and anti conformation of hydroxyl
p
ribbons are joined by weak C –H O and C B interactions as
…
p
…
shown in Fig. 2b. In (2) weak interactions lead to a 2-D
Table 1 The geometry of intra- and intermolecular interactions in
˚
crystals of 2-alkoxyphenylboronic acids [A, u]
…
…
…
D–H A
H
A
D
A
1
O12–H12 O11
O11–H11 O2
…
…
a
c
1.92(2)
1.94(2)
2.781(1)
2.654(2)
177(2)
140(2)
b
2
O12–H12 O11
…
…
1.89(2)
1.93(2)
2.780(1)
2.664(1)
169(2)
142(2)
b
O11–H11 O2
3
O12A–H12A O11B
…
…
d
1.96(2)
1.89(2)
1.87(2)
1.95(2)
2.840(2)
2.622(2)
2.752(2)
2.663(2)
c
139(1)
141(2)
168(2)
143(2)
b
O11A–H11A O2A
O12B–H12B O11A
…
d
Fig. 1 Dimeric molecular motifs observed in the structures of (1), (2)
and (3). In the case of (1) and (2) dimers are centrosymmetric while (3) is
not. Bulky atoms represent the aliphatic chain: methyl-, ethyl- or
isobutyl-.
…
b
O11B–H11B O2B
a
b
symmetry codes: 1 2 x, 2y, 2 2 z; x, y, z; 1 2 x, 1 2 y, 1 2 z;
d
x, 1.5 2 y, 20.5 + z
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¯
¯
Fig. 2 a) Ribbon motif in the (141) plane in (1). b) The crystal packing along the [101] direction in (1). c) 2-D layer on (103) plane in (2). d) The crystal
packing along the [010] direction in (2). e) The crystal packing along the [100] direction in (3).
¯
structure, with molecules forming layers in the (103) plane.
methoxy groups at ortho positions. Instead, the dimers interact
p
…
…
…
p
Within such layers, weak C H O, B O or B C interactions
are present collecting the dimers together (Fig. 2c–d). In (3) the
intermolecular interactions lead to complex 3-D structures
with the other pair of dimers and form infinite ribbons along the
…
…
[001] direction with the distances O11–H11 O119 and O11 O119
˚
equal to 2.00(2) A and 2.729(2) A, respectively. The ribbons interact
˚
…
p
p
…
p
…
p
…
involving both CH C , C H B or C B interactions (see
Fig. 2e).
further in the crystal lattice by weak C H O interactions, which
involve a meta phenyl hydrogen and methoxy group or a para
phenyl hydrogen and hydroxyl groups of two other units. The latter
is bifurcated as shown in Fig. 4a.
B. 2,6-Dialkoxyphenylboronic acids. 2,6-Dimethoxyphenylboronic
acid forms two polymorphs. One of them crystallizes in tetragonal
¯
P4n2 (4A) and the other one in the C2/c space group (4B). The
Polymorph II (4B) reveals a completely novel type of crystal
packing. It consists of two kinds of molecules. One of them (A)
displays two intramolecular hydrogen bonds between hydroxyl
groups of a boronic fragment and the proximal methoxy groups
(Fig. 3b). Notably, they are even shorter than in monosub-
former consists of half of the molecule in an independent part of the
unit cell, while the latter is composed of one-and-a-half molecules.
Most importantly, the crystal packing is completely different in
both cases. Polymorph I (4A) forms classic dimers, as shown in
…
stituted parent systems: the OH O distances are 1.90(3)–1.92(3)
˚
…
˚
Fig. 3a. They have D symmetry because they lay on three 2-fold
2
A while the respective O O distances are 2.615(2)–2.621(2) A,
which suggests that they are more effective. Moreover, the
boronic group is twisted with respect to the phenyl fragment by
6.9u, which is similar to the parent monosubstituted analogue. It
should however be noted that one of the hydroxyl groups may
serve as a hydrogen bond donor in an intermolecular hydrogen
bond to a hydroxyl group of a molecule related by a center of
axes. This forces the hydrogen atoms of the boronic group to be
disordered. The hydrogen bonds in the dimers are even shorter than
…
in (1)–(3) with the O11–H11 O119 and O11 O119 distances equal
…
˚
˚
to 1.93(2) A and 2.748(2) A, respectively (see Table 2). The phenyl
rings are twisted with respect to the boronic groups by 46.3u which
disables the intramolecular hydrogen bond formation with
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Fig. 3 Molecular structure of 2,6-dimethoxyphenylboronic acid: a) Polymorph I (4A). b) Polymorph II (4B).
…
inversion (2 2 x, 2y, 1 2 z); however, the O11A–H11A O11A9
Also 2,6-diethoxyphenylboronic acid exists in two polymorphs
which differ in volume of the unit cell, and most importantly,
have totally different molecular interactions. Both systems
˚
distance is rather long at 2.557(2) A (the relevant O11A O11A9
…
˚
distance is 3.008 A). The other molecule (B) lays on a 2-fold axis.
In this case the ring is twisted by 60u with respect to the boronic
group and the two hydroxyl hydrogen atoms are in anti
conformations. They are donors of hydrogen bonds to one of
hydroxyl groups of two adjacent (A) type molecules, forming
rather unusual trimers, as shown in Fig. 3b. The respective
1
crystallize in the monoclinic P2 /c space group. However,
polymorph I (5A) consists of one molecule, while polymorph II
(5B) comprises four independent molecules in the asymmetric
part of the unit cell. The former forms an infinite ladder where
the participating molecules are shifted with respect to each other
…
O11B–H11B O12A and O11B O12A distances equal to
…
along the 2 axis (Fig. 5a). This is not a very common motif in
1
˚ ˚
.88(3) A and 2.781(2) A. The resulting packing along the
¯
110] direction is shown in Fig. 4b. It is clear that monomers are
the structures of phenylboronic acids, although it has already
1
1
5
been observed in 4-methoxyphenylboronic acid
and 1,2-
[
3
2
ethynediylbis(4,1-phenylene)diboronic acid. Again the boronic
group is highly twisted with respect to the phenyl ring (by 51u),
which disables intramolecular hydrogen bond formation. The
intermolecular hydrogen bond lengths are somewhat shorter
than those observed for monosubstituted species. The O11–
the dominant motif while the dimers are not present in the
structure at all.
Table 2 The geometry of intra- and intermolecular interactions in
˚
…
˚
H11 O12 distance between pairs of shifted units is 1.79(2) A
crystals of 2,6-dialkoxyphenylboronic acids [A, u]
…
the O11 O12 distance is 2.746(1) A), while it is O12–
˚
(
…
…
…
D–H A
H
A
D
A
…
H12 O11 2.02(2) A between parallel units (the respective
˚
…
O12 O11 distance is 2.727(2) A, see Table 2 for details). The
˚
4
A
a
b
…
p
…
…
…
O11–H11 O119
O11–H11 O119
4
1.93(2)
2.00(2) A
2.748(2)
2.729(2)
158(3)
141(2)
crystal structure is further stabilized by weak CH C or CH
interactions. The packing is shown in Fig. 6a.
B
˚
B
c
c
Polymorph II (5B) possesses quite different packing. All
boronic groups are twisted with respect to phenyl rings by a
much smaller extent (6.4u, 3.4u, 9.6u or 9.3u for A–D) and all
O11A–H11A..O2A
1.92(3)
1.90(3)
1.88(3)
2.621(2)
2.615(2)
2.781(2)
143(2)
145(2)
175(2)
O12A–H12A..O6A
…
d
O11B–H11B O12A
5
A
hydroxy groups are in the anti conformation. The intramolecular
…
…
…
e
f
O11–H11 O12
O12–H12 O11
5
O11A–H11A O2A
O12A–H12A O6A
O11B–H11B O2B
O12B–H12B O6B
O11C–H11C O2C
O12C–H12C O6C
O11D–H11D O2D
…
O12D–H12D O6D
6
O11–H11 O2
O12–H12 O6
1.79(2)
2.02(2)
2.746(1)
2.727(1)
165(2)
142(2)
O
O distances vary in a rather broad range (between 2.632(2)–
˚
B
2.657(2) A, see Table 2), but again they are shorter than in the
parent monosubstituted system. Importantly, solely intramole-
cular hydrogen bonds are observed! The molecules A and C and
…
…
…
…
…
1.91(2)
1.95(2)
1.95(2)
1.90(2)
1.89(2)
1.91(3)
2.00(3)
1.91(2)
2.634 (2)
2.653(2)
2.651(2)
2.632(2)
2.632(3)
2.653(2)
2.657(2)
2.646(2)
141(2)
139(2)
142(2)
144(2)
145(2)
144(3)
138(2)
142(2)
¯
B and D form very similar layers in (101) planes, where the
molecules and planes are joined by weak intermolecular
…
…
p
p
…
…
…
C H O, CH O or C H B interactions only (see Fig. 6b–d).
This is an even more striking packing motif than in 2,6-
dimethoxyphenylboronic acid, polymorph II (4B), where there is
no dimer formation at all!
…
…
1.93(2)
1.91(2)
2.640(1)
2.635(1)
144(2)
139(2)
Finally, a very similar pattern is observed in the crystal
structure of 2-isobutoxy-6-methoxyphenylboronic acid (6)
a
symmetry codes: 1.5 2 y, 1.5 2 x, 1.5 2 z; x, y, 1 + z; x, y, z;
b
c
d
e
.5 2 x, 0.5 2 y, 1 2 z; 1.5 2 x, 20.5 + y, 0.5 2 z; x, 1 + y, z;
f
1
(
Fig. 7). This molecule crystallizes as monoclinic P2
1
/n with
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¯
Fig. 4 a) The crystal packing along the [001] direction in (4A). b) The crystal packing along the [110] direction in (4B).
3
3
one molecule in the asymmetric part of the unit cell. Again the
boronic group is almost coplanar with the phenyl ring (the twist
is 4.3u) and both hydrogen atoms at hydroxyl groups are in the
anti conformation, which leads to intramolecular hydrogen bond
formation. Despite the different bulkiness of the alkoxy groups,
Hirshfeld surfaces. Internal (d ) and external (d ) distances
i e
between atoms serve to create a surface which can easily
demonstrate differences between polymorphs and more generally
the different packing motifs based on the fingerprints of selected
interactions. The phenylboronic acid structures analyzed in this
paper form dimers, ladders or even monomers. It is particularly
interesting to link the type of the structural motif with a 2-D
fingerprint plot based on the Hirshfeld surface analysis. Even
disordered structures [H-disordered (4A), ethyl group disordered
(5A)] were included in the investigations of the fingerprint plots,
but these data should be treated with some care.
…
…
the O11 O6 and O12 O2 distances are very similar: 2.635(1) A
˚
˚
and 2.640(1) A. The elongation in the latter case may be caused
by a possible intermolecular interaction with another hydroxyl
…
group of a molecule related by a center of inversion (the O
O
˚
distance is 2.911(1) A). This might be the only significant
intermolecular hydrogen bond interaction which contributes to
the overall stability of the crystal structure. The other minor
The comparison of the fingerprint plots for separate moieties
present in the structures is presented in Fig. 8. It can be easily
seen that, for the first three structures of phenyl boronic acid
derivatives (see Fig. 8a–d), very sharp and symmetrical tails are
formed. This results from strong intermolecular interactions
…
p
…
…
contributions again come from CH C , CH O or CH
weak interactions.
B
Analysis of fingerprints based on the Hirshfeld surfaces
…
between O–H O atoms which are present in the dimers. The
The ideal way to compare similar crystal structures is the
analysis of interactions in the crystal lattice based on the
symmetrical shape of these plots also indicates that all oxygen
atoms in the boronic groups are simultaneously donors and
Fig. 5 Molecular structure of 2,6-diethoxyphenylboronic acid: a) Polymorph I (5A). b) Polymorph II (5B).
6
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¯
Fig. 6 a) The crystal packing along the [010] direction in (5A). b) The crystal packing along the [010] direction in (5B). c) 2-D layer in the (101) plane
¯
formed by molecules A and C. d) 2-D layer in the (101) plane formed by molecules B and D.
acceptors of hydrogen bonds. For the structure (4A) a somewhat
strange but rather symmetrical fingerprint plot is observed (see
Fig. 8e). The reason for this is the disorder of hydrogen atoms in
hydroxyl groups, which is enforced by the special position in the
cannot play both of these roles. For the structure (5A), due to
disorder in the ethyl chain, two alternative fingerprint plots were
…
prepared (i and j). In the plot (i) short H H contacts can be
observed (gray scattered spots for smaller d and d ) which is due
e i
¯
P4n2 space group. To get further insight into this fingerprint, we
to intermolecular contact distances between ethyl chains which
are too close, even in modeled ordered structure variant I. Both
plots are symmetrical as all oxygen atoms of hydroxyl groups are
simultaneously donors and acceptors of hydrogen bonds. It is
noteworthy that these plots are rather similar to the one
generated for the ordered structure (4A). Also in this case a
broadening of the tails is clear. This is due to the formation of a
ladder-type motif in the crystal lattice where the molecules form
an infinite chain. Finally the last five 2-D plots (Fig. 8k–o) nicely
have artificially ordered all hydrogen atoms by doing a
transformation to the P1 space group and by removing all
redundant hydrogen atoms at hydroxyl groups. Fig. 8f presents
the 2-D fingerprint for one of these tricky ordering cases. The
picture now resembles the plots for (1), (2) or (3) with strong O–
H contacts observed in the form of long and symmetrical tails. In
this case (4A) the tails are slightly wider, and result from the
…
polymeric hydrogen bonded structure where the O H interac-
…
illustrate the lack of any strong O H interactions in the
tions are present along linearly-independent directions. For the
next (4B) structure two 2-D fingerprints plots (Fig. 8g–h) can be
obtained for each symmetry independent moiety in the crystal
lattice. Here the plots are non-symmetrical with only one sharp
investigated structures for four molecules in (5B) and one
molecule in (6), respectively. Thus these plots are characteristic
of purely monomeric motifs in these types of structures.
…
tail representing a strong O–H O contact present in the linear
Calculations
trimer. The asymmetrical nature of the plot is due to the fact that
molecules in the trimer are either donors or acceptors of HB but
What is the reason for the great variability of observed crystal
structure types? The answer is given by the analysis of the
interaction energies, most importantly in the case of hydrogen
bonds.
The strength of the intramolecular hydrogen bond can be
estimated using a simple homodesmotic reaction (see eqn (1) and
3
2)). This is a theoretical approach, where on the right side of
4
(
the reaction scheme one of the compounds contains two
molecular fragments interacting with each other, whereas on
its left side the fragments are separated. Benzene has been added
to fulfill homodesmotic reaction requirements. This kind of
theoretical approach has been extremely fruitful in the estimation
Fig. 7 a) Molecular structure of 2-isobutoxy-6-methoxyphenylboronic
acid. b) Interactions in the crystal lattice - view along [001].
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Fig. 8 Fingerprint plots visualizing d
e
and d
i
for O and H atoms (including reciprocal ones) generated for structures a) (1). b) (2). c) (3) molecule A. d)
¯
(
(
3) molecule B. e) (4A) H-disordered molecule. f) (4A) H-ordered molecule modelled in P1 space group based on P4n2 structure. g) (4B) molecule A. h)
4B) molecule B. i) (5A) ethyl-ordered variant I. j) (5A) ethyl-ordered variant II. k) (5B) molecule A. l) (5B) molecule B. m) (5B) molecule C. n) (5B)
molecule D. o) (6). On each plot the percentage contribution of O and H distances is given.
3
5
of many subtle energetic effects in physical organic chemistry,
3
6
like aromatic stabilization energies or substituent effect stabili-
3
zation energies. Most recently it was used to analyze substituent
ð1Þ
7
effects on intramolecular hydrogen bond or dative bond forma-
3
tion in imino- and aminomethylphenylboronic acids.
8
6
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21
Table 3 The energies of intramolecular hydrogen bonds in phenylboronic dimers [given in kcal mol ]. The symmetry refers to the most stable
conformation (optimal) at B3LYP/62311+G** level. The values optimised at MP2/6231+G* are given in brackets
System
Symm.
Energy
b
System
Symm.
Energy
8.6 [11.9]
9.6 [14.7]
R
1
R
1
R
1
= OC
= OCH
= OC
2
H
5
, R
, R
, R
2
= H
= OCH
= OC
C
C
C
2h
9.6 [14.8]
8.5
8.7
a
b
R
R
a
1
= H, R
= OCH
2
= H
, R
C
C
i
3
2
3
i
i
1
3
2
= H
2h
2
H
5
2
2
H
5
21
3.5 kcal mol if not corrected for ZPE. Value not corrected for ZPE.
b
1
The energies of intermolecular hydrogen bonds were calcu-
lated by comparison of the energies of dimers of phenylboronic
acid, 2-methoxyphenylboronic acid, 2-ethoxyphenylboronic
acid, 2,6-dimethoxyphenylboronic acid and 2,6-diethoxyphenyl-
boronic acid with their fully-optimised monomeric fragments,
taking into account basis-set superposition error (for details see
the experimental part and the ESI{). The resulting energies are
given in Table 3.
ð2Þ
The energy of the intramolecular hydrogen bond in 2-meth-
oxy- or 2-ethoxyphenylboronic acid is virtually independent of
2
the alkane chain length, being 3.8 kcal mol in both cases (at
1
2
1
B3LYP/6-311+G** level) or 5.4–5.7 kcal mol , respectively (at
MP2/6-31+G* level), based on eqn (1)). Interestingly, the
introduction of a second methoxy- (or ethoxy-) group at the
ortho position does not double the interaction energy value.
Instead, it seems to cause a negative synergism. The resulting
It is clear that the energies of hydrogen bonds vary over a very
2
1
small range: 8.5–9.6 kcal mol (at B3LYP/6-2311+G**) and
do not depend on the length of the alkyl chain. The value of the
interaction energy in the parent phenylboronic acid is consistent
2
1
energy values are 5.6 at kcal mol (at B3LYP/6-311+G** level)
2
or 7.4 or 8.3 kcal mol (at MP2/6-31+G* level), respectively, in
,6-dimethoxy- or 2,6-diethoxyphenylboronic acid. This result
4
0
1
with the value estimated earlier by Rodriguez-Cuamatzi et al.,
1
9
and more recently by our group. Smaller values of interaction
energies in the case of di-ortho-substituted systems can be
attributed to repulsive interactions between lone pairs at oxygens
of the hydroxy groups involved in intermolecular hydrogen
bonds and the oxygen of the ortho-alkoxy group. This is
accompanied by lowering the formal symmetry from C2h
2
might be attributed, at least in part, to repulsive steric
interactions between the hydrogen atom of the hydroxyl group
and hydrogen atom(s) in ortho position(s) in the benzene ring of
phenylboronic acid. This effect leads to a twist of the boronic
group in respect to the phenyl fragment and to the elongation of
the C–B bond. If planarity of reference compounds is enforced
(
ortho-alkoxyphenylboronic acid dimer) to C . So the intermo-
i
2
1
2
1
lecular interaction energy is ca. 4–5 kcal mol per hydrogen
bond.
then the estimated energy values rise up to 5.9 kcal mol (at
2
1
B3LYP/6-311+G** level) or 8.2 or 9.2 kcal mol (at MP2/6-
1+G* level) for 2,6-dimethoxy- or 2,6-diethoxyphenylboronic
In the structure of phenylboronic acids one more important
interaction has to be taken into account. The dimers interact
3
3
acid, respectively. Based on these data it is safe to conclude that
9
the energy of a single intramolecular hydrogen bond in ortho-
2
1
alkoxyphenyl boronic acid is approximately 4-5 kcal mol at
this level of theory.
Fig. 10 Two kinds of ortho-methoxyphenylboronic acid dimers (a) with
two intramolecular hydrogen bonds, (b) with two repulsive interactions
between proximal oxygen atoms.
Fig. 9 The phenylboronic acid tetramer optimised from 2,6-di-methox-
yphenylboronic acid, polymorph I.
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with the neighbouring dimeric units in the crystal lattice. One of
the possibilities is that the dimer interacts with four other dimeric
units which are twisted with respect to the given unit. This kind
of motif has been observed in the structure of the parent
This kind of structure is observed e.g. in the case of 2,6-
dimethoxyphenylboronic acid, polymorph I discussed in this
report (see Fig. 3). Starting from the experimental data of this
2
system we have optimised the tetramer having C symmetry at
1
1,19,41
phenylboronic acid
Another basic arrangement is noticed
the B3LYP/62311+G** level. To avoid unwanted possible
interactions involving methoxy groups, they were replaced by
hydrogen atoms as shown in Fig. 9.
if a dimer interacts with another two dimers which are situated
parallel to each other. Infinite ribbons are formed in this way.
Fig. 11 Thermal ellipsoid plot of all moieties in structures (1), (2), (3), (4A), (4B), (5A), (5B) and (6). All plots are on the same scale and present ADPs
at the 50% probability level.
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Table 4 Crystal data and structure refinement for: 2-methoxyphenylboronic acid (1), 2-ethoxyphenylboronic acid (2) and 2-isobutoxyphenylboronic
acid (3)
Compound
(1)
(2)
(3)
Empirical formula
Formula weight
Space group
C
7
H
9
BO
151.95
P2 /c
3
C
8
H
11BO
165.98
P2 /n
3
C
10
H
15BO
194.03
P2 /c
3
1
1
1
Unit cell dimensions
˚
a [A]
˚
7.718 (1)
14.454 (1)
7.284 (1)
113.43 (1)
745.5 (1)
4
1.354
0.102
2.82–27.16
29 , = h , = 9
5.418 (1)
12.909(2)
12.984(2)
18.437(3)
134.64(3)
2198.9 (8)
8
1.173
0.083
3.11–25.50
215 , = h , = 15
213 , = k , = 15
222 , = l , = 22
16 486/4084
4084/374
b [A]
˚
c [A]
14.812 (3)
10.728 (2)
103.29 (3)
837.9 (3)
4
1.316
0.097
3.90–25.49
26 , = h , = 5
217 , = k , = 17
212 , = l , = 12
6271/1551
1551/153
b [u]
Volume V [A ]
Z [molecules/cell]
3
˚
2
3
Dcalculated [Mg m
]
Absorption coefficient m/mm
2
1
h range for data collection [u]
Limiting indices
2
2
18 , = k , = 18
9 , = l , = 9
Reflections collected/unique
Data/parameters
Goodness of Fit
7983/1610
1610/136
1.045
0.0381
0.1163
0.253 and 20.323
1.091
0.0341
0.0908
0.217 and 20.275
1.003
0.0399
0.0809
0.189 and 20.167
Final R index (I . 2s)
wR
2
2
3
]
˚
Largest diff. peak and hole [A
Based on the energies of a tetramer and two neighbouring
dimers (BSSE corrected) we have estimated the energy of
shown in Fig. 10. Although the interaction energies within the
2
1
21
dimers are comparable (8.3 kcal mol versus 9.6 kcal mol ), the
2
interaction between the dimers as 8.5 kcal mol , which equates
1
21
(b) unit is less stable by 13.9 kcal mol than (a), both for ortho-
2
1
to around 4 kcal mol
per hydrogen bond. Yet another
methoxy or ortho-ethoxy phenylboronic acid dimers. The reason
estimation based on pairs of phenylboronic acids not involved in
the dimers (left and right pair of the acids) led to the value of
is not only the stabilization effect of two intramolecular hydrogen
2
1
bonds in (a) (2 6 4–5 kcal mol ) but also two unfavourable
repulsive interactions between lone pairs at proximal oxygen
atoms in (b). To minimize the latter effect, the phenyl ring twists
with respect to the boronic group by 50.9u (2-methoxyphenyl-
boronic acid dimer) or 51.4u (2-ethoxyphenylboronic acid dimer,
(b) type), exactly as in the structure of 2,6-dimethoxyphenylboro-
nic acid, polymorph I, where the angle between the mean planes of
the boronic group and the phenyl ring is 46.3u.
2
8.1 kcal mol , which gives 4.5 kcal mol
1
21
1
of energy per
hydrogen bond forming the dimer. This is fully consistent with
the data presented above.
Finally, it is instructive to compare the energies of two
symmetric ortho-methoxy (or ortho-ethoxy) phenylboronic acid
dimers, where one of them has hydroxyl groups at ortho-positions
enabling or disabling intramolecular hydrogen bond formation, as
Table 5 Crystal data and structure refinement for: 2,6-dimethoxyphenylboronic acid, polymorph I (4A), 2,6-dimethoxyphenylboronic acid,
polymorph II (4B), 2,6-diethoxyphenylboronic acid, polymorph I (5A), 2,6-diethoxyphenylboronic acid, polymorph II (5B) and 2-isobutoxy-6-
methoxyphenylboronic acid (6)
Compound
(4A)
(4B)
(5A)
(5B)
(6)
Empirical formula
Formula weight
Space group
C
181.98
¯
P4n2
8
H
11BO
4
C
181.98
C2/c
8
H
11BO
4
C
10
H
15BO
210.03
P2 /n
4
C
10
H
15BO
210.03
P2 /c
4
C
11
H
17BO
224.06
P2 /n
4
1
1
1
Unit cell dimensions
˚
a [A]
˚
13.376 (1)
13.376 (1)
5.033 (1)
14.405(1)
8.471(1)
22.271(1)
98.17(1)
2690.1(3)
12
1.348
0.105
2.88–25.50
15.188(2)
5.0173(5)
15.737(2)
117.18(2)
1066.8(2)
4
1.308
0.098
2.91–27.50
20.081(1)
15.533(1)
15.096(1)
109.72(1)
4432.5(3)
16
1.259
0.094
3.15–25.50
7.571 (1)
14.670 (2)
10.660 (2)
91.73(1)
1183.5(3)
4
b [A]
˚
c [A]
b [u]
Volume V [A ]
Z [molecules/cell]
3
˚
900.5(1)
4
1.342
0.105
3.05–25.48
2
3
Dcalculated [Mg m
]
Absorption coefficient m/mm
1.257
0.093
2
1
h range for data collection [u]
Limiting indices
3.35–25.50
216 , = h , = 15 217 , = h , = 17 219 , = h , = 17 0 221 , = h , = 24 29 , = h , = 9
216 , = k , = 16 210 , = k , = 10 , = k , = 6 0
218 , = k , = 18 216 , = k , = 17
2
6 , = l , = 6
226 , = l , = 26
10 471/2496
2496/245
0.991
0.0430
, = l , = 20
2447/2447
2447/154
1.102
0.0426
218 , = l , = 18
34 808/8231
8231/781
1.036
0.0452
212 , = l , = 12
8321/2182
2181/214
1.106
0.0415
Reflections collected/unique
Data/parameters
Goodness of Fit
6907/847
847/89
1.017
0.0232
0.0565
0.225 and 20.103
Final R index (I . 2s)
wR
˚
Largest diff. peak and hole [A
2
0.0667
0.186 and 20.140
0.1372
0.391 and 20.229
0.0917
0.286 and 20.210
0.1102
0.249 and 20.226
2
3
]
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It is fair to note that the energy values of the most important
interactions observed in the crystal lattices of ortho-alkoxyphenylboronic
acids are very similar. All kinds of hydrogen bonds have energies
efficiently influence the crystal packing. For this reason we expect
that these kinds of systems will be commonly used as important
building blocks to obtain new types of structures in supramolecular
chemistry and/or crystal engineering. Their flexibility towards diverse
interactions and variability towards various structure formation may
also have an immense practical importance, as ortho- substituted aryl
2
1
around 4–5 kcal mol per interaction. The repulsive interactions
between oxygen lone pairs are significantly weaker and their
influence is reduced by conformational adjustments of the
molecules or their dimers in the crystal lattice. Therefore the
competition between intra- and intermolecular interactions in
the crystal lattices is very efficient and explains why many diverse
structures may be formed. Even small structural effects, like e.g.
change of solvent or thermodynamic conditions may easily
influence the crystal packing.
42,43
monoboronic acids are commonly used in sugar recognition.
44
Boron is often called ‘‘the least boring element’’ by its aficionados.
We expect that the same applies to ortho-alkoxyboronic (or di-ortho-
alkoxyboronic acids) in the boronic acids family.
Experimental
Synthesis of 5
Conclusions
a) 1,3-Diethoxybenzene. To a mixture of 35.73 g (0.324 mol) of
resorcinol, 4.20 g (0.013 mol) of TBAB and 28.50 g (0.710 mol)
of NaOH in 250 ml of water, 105.90 g (0.972 mol) of ethyl
bromide was added. The mixture was refluxed with stirring for
In this report we have studied crystal structures of three
2
-alkoxy-substituted phenylboronic acids and three 2,6-dia-
lkoxy-substituted phenylboronic acids with methoxy, ethoxy or
isobutoxy groups. The former species served as reference
structures for the latter ones. The molecules in monosubstituted
derivatives (1)–(3) interact with each other by intermolecular
hydrogen bonds to form dimers, the most common motif of
phenylboronic acids. The participating molecules are stabilized
by intramolecular hydrogen bonds involving hydroxyl groups in
the anti position and the alkoxy group in the proximal position.
A much wider variety of possible types of interactions has been
found in the disubstituted species. Two of them: 2,6-dimethox-
yphenylboronic acid and 2,6-diethoxyphenylboronic acid form
two polymorphs each. In three crystal structures we have found
unprecedented packing, where the predominant motifs are
monomers. In 2,6-diethoxyphenylboronic acid, polymorph II
5
1
h. After cooling, the organic layer was separated, washed with
M aq. NaOH and finally several times with water to obtain
neutral pH. Volatiles were evaporated under vacuum to obtain
2.84 g (0.20 mol, 61.7%) of crude 1,3-diethoxybenzene, which
3
1
was used without further purification. H NMR (400 MHz,
CDCl ) d: 7.11 (m, 1H), 6.44 (m, 3H), 3.94 (q, 4H), 1.36 (t, 6H).
3
b) 2,6-Diethoxyphenylboronic acid (5). The reaction was
carried out under an argon atmosphere. To a solution of
3
2.84 g (0.20 mol) of 1,3-diethoxybenzene in 170 ml of ether
placed in 3-necked vessel equipped with CO /acetone bath,
2
magnetic stirrer, dropping funnel and thermometer, 23.9 g
(
31 ml, 0.206 mol) of TMEDA was added. The mixture was
cooled down to 220 uC. n-Butyllithium (10 M, 20 ml, 0.20 mol)
was dropped-in while keeping the temperature below 210 uC.
After 1 h of stirring at that temperature, the mixture was cooled
down to 265 uC and 30.07 g of triethyl borate (35 ml, 0.206 mol)
was dropped-in while keeping the temperature below 260 uC.
The mixture was left overnight at RT, cooled down to 220 uC,
(
5B) the molecular environment disables any other types of
intermolecular interactions, except very weak ones. In the
structure of 2,6-dimethoxyphenylboronic acid, polymorph II
(
4B), one of the independent molecules form monomers while the
other one plays the role of a bridge which links two monomers.
Yet another molecule: 2-isobutoxy-6-methoxyphenylboronic
acid shows peculiar crystal packing with only monomers present
in the crystal lattice. The remaining polymorphs of 2,6-
dimethoxyphenylboronic acid or 2,6-diethoxyphenylboronic acid
form dimers (4A) or ladders (5A) respectively – a rather
uncommon molecular motif in phenylboronic acids, but already
known. Different structural motifs present in the solid state were
illustrated and described by analysis of the fingerprints based on
the Hirshfeld surfaces. Four types of plots are associated with
the presented structures. For the dimeric motif, the characteristic
tails are long and sharp. For both the polymeric ladder or ribbon
type of motifs, a slight broadening of these long tails is observed.
For the purely monomeric structures there are only short and
wide peaks. All of these three types of plots are symmetric. A
non-symmetrical type of fingerprint plot has been found only for
the trimer motif, where oxygen atoms of hydroxyl groups can
play the role of hydrogen bond donor or acceptor.
2 4
and hydrolyzed with 1.5 M aq. H SO . The aqueous layer was
extracted with 2 6 60 ml of ether. The organic phases were
combined and about 3/4 of the volume of the solvent removed
under reduced pressure. Water (50 ml) was added to the remaining
liquid and evaporation was continued for an additional half an
hour. The yellowish solid was filtered-off and dried in air to obtain
1
0.0 g (48.7%) of the product. H NMR (400 MHz, acetone-d ) d
2
6
1
1
(
ppm): 7.36 (m, 1H), 6.70 (m, 2H), 4.16 (q, 4H), 1.42 (t, 6H).
B
NMR (128.3 MHz, acetone-d ) d (ppm): 35.0.
6
2
-Methoxyphenylboronic acid (1), 2-ethoxyphenylboronic
acid (2), 2-isobutoxyphenylboronic acid (3), 2,6-dimethoxyphe-
nylboronic acid (4) and 2-isobutoxy-6-methoxyphenylboronic
acid (6) were obtained from Aldrich.
Crystallization
The crystallizations were performed by slow evaporation from
methanol, ethanol, methanol/water, ethanol/water or hexane
solutions. Suitable crystals for X-ray diffraction experiment were
obtained from ethanol solutions. In the case of 2,6-diethox-
yphenylboronic acid, two distinct types of single crystals were
obtained. They differed in morphology (i.e. long needle (5A) and
prism (5B)) and were found to be two polymorphs. In turn, the
The varieties of possible types of interactions were analyzed by
interaction energies, which have been estimated to be very similar
for both intra- and intermolecular hydrogen bonds in the studied
systems. From this point of view they are highly competitive and
molecules are ‘‘at the edge’’. Hence many diverse structures can be
formed and small structural or environmental effects may
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crystallization from hexane solution was successful only in one
case i.e. 2,6-dimethoxyphenylboronic acid. Its structural analysis
revealed a second polymorph of the acid (4B).
energies in their homodimers, and the parent phenylboronic acid
dimer, were initially optimised at MP2/6231+G* level of
5
2
theory starting from the most stable conformers (see the
ESI{ for details). Due to convergence problems in the case of the
latter systems (except for dimers of phenylboronic acid,
X-ray diffraction
2
-methoxyphenylboronic acid 2-ethoxyphenylboronic acid) all
The X-ray measurements of 2-methoxyphenylboronic acid (1),
systems were also optimised at the B3LYP/62311+G** level of
theory. The structures so obtained corresponded to real minima
on the potential energy surfaces as checked by frequency
calculations at corresponding levels of theory MP2/6231+G*
or B3LYP/62311+G**, respectively. The energy values (except
two cases, see Table 3) were corrected for vibrational zero point
energy correction (ZPE). Although the estimated values of
hydrogen bond energies (corrected by basis-set superposition
error (BSSE) in the case of intermolecular interactions) were
slightly larger at MP2/6-31+G* as compared with B3LYP/
2
-ethoxyphenylboronic acid (2) 2-isobutoxyphenylboronic acid (3),
,6-dimethoxyphenylboronic acid, polymorph (4A), 2,6-
2
I
dimethoxyphenylboronic acid, polymorph II (4B), 2,6-diethoxy-
phenylboronic acid, polymorph I (5A), 2,6-diethoxyphenylboronic
acid, polymorph II (5B) and 2-isobutoxy-6-methoxyphenylboronic
acid (6) were performed at 100 (2) K on a KUMA CCD k-axis
diffractometer with graphite-monochromated Mo Ka radiation
˚
(0.71073 A) (see Fig. 11 for thermal ellipsoid plots). The crystals of
(1), (2), (3), (4A), (4B), (5A), (5B) and (6) were positioned 62.25 mm
from the KM4CCD camera; 1920 frames were measured at 0.8u
intervals on a counting time of 2s, 748 frames were measured at 0.8u
intervals with a counting time of 25s, 748 frames were measured at
62311+G** level, their relative values fit each other almost
perfectly. The correlation coefficient for the dependence between
the energies estimated at two levels of theory is equal R = 0.9886
0.8u intervals with a counting time of 20s, 748 frames were
(
see Fig. S1 and Fig. S2 in the ESI{).
measured at 0.8u intervals with a counting time of 25s, 1200 frames
were measured at 0.5u intervals with a counting time of 25s, 1200
frames were measured at 0.5u intervals with a counting time of 15s,
Acknowledgements
8
56 frames were measured at 0.7u intervals with a counting time of
5s, and 664 frames were measured at 0.9u intervals with a counting
We dedicate this paper to Professor Tadeusz Marek Krygowski
on the occasion of his 75th birthday. The X-ray structures were
measured in the Crystallography Unit of the Physical Chemistry
Laboratory at the Chemistry Department of the University of
Warsaw. The Interdisciplinary Centre for Mathematical and
Computational Modeling (Warsaw, Poland) provided computa-
tional facilities. P.K. and D.K.S. gratefully acknowledge Dr
Łukasz Dobrzycki (University of Warsaw) for useful comments.
This research was supported by the Ministry of Science and
Higher Education (grant N204 01932/0614) and partially by the
Aldrich Chemical Co. Inc., Milwaukee, Wisconsin through the
donation of chemicals and equipment. A.S. and J.S. acknowl-
edge the financial support from Warsaw University of
Technology. Finally, we thank Dr Sian Howard for reading
and suggesting corrections to the manuscript.
2
time of 3s, respectively for (1)–(6). Data collection, cell refinement
and data reduction were carried out with the KUMA Diffraction
45
programs: CrysAlis CCD and CrysAlis RED. The data were
corrected for Lorentz and polarization effects, but no absorption
correction was applied. The structure was solved by direct
46
47
methods and refined by using SHELXL. The refinement was
2
based on F for all reflections except for those with very negative F .
2
The weighted R factor, wR and all goodness-of-fit S values are
2
based on F . The non-hydrogen atoms were refined anisotropically.
The hydrogen atoms were located from a difference map and were
refined isotropically. The atomic scattering factors were taken from
48
the International Tables. Crystal structure and structural refine-
ment are specified in Tables 4–5. In the case of 2,6-dimethoxyphe-
nylboronic acid, polymorph I (4A) the hydrogen atoms forming the
dimers were disordered due to their position on a 2-fold axis. In the
case of 2,6-diethoxyphenylboronic acid the crystals of (5A) were
twinned by reticular pseudomerohedry with a twin obliquity of
References
1 J. W. Steed and J. L. Atwood, Supramolecular Chemistry, 2nd
edition, 2009, John Wiley & Sons, Chichester.
2.29(1)u. During data reduction two twin components were included
2
3
G. R. Desiraju, Angew. Chem., Int. Ed. Engl., 1995, 34, 2311–2327.
For a review see: N. Miyaura and A. Suzuki, Chem. Rev., 1995, 95,
with the ratio yielding 0.49 : 0.51. After the final HKLF 5 refinement
the twinning effect was included in the reflection file and the final
HKLF 4 refinement based on the merged data were carried out. The
structure of (5A) is disordered with one of the ethyl chains occupying
two alternative sites with 50% occupancy each. A full list of bond
lengths, bond angles and torsion angles is given in Tables 1–9 in the
ESI.{ Analysis of fingerprints based on the Hirshfeld surfaces was
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This journal is ß The Royal Society of Chemistry 2012