Halogen bond effect on bundling of hydrogen bonded 2-fold helical columns

Article abstract of DOI:10.1039/c2ce26081f

Bundling of the hydrogen bonded 2-fold helical columns has been altered on the basis of a robust halogen bond between an iodine and anionic oxygen atom. This alteration causes a change of the space groups of the resulting crystals.

Full text of DOI:10.1039/c2ce26081f

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Bundling of the hydrogen bonded 2-fold helical columns has been altered on the basis of a robust
halogen bond between an iodine and anionic oxygen atom. This alteration causes a change of the
space groups of the resulting crystals.

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ARTICLE TYPE
Halogen bond effect on bundling of hydrogen bonded 2-fold helical
columns
Toshiyuki Sasaki,a Ichiro Hisaki,*a Seiji Tsuzuki,b Norimitsu Tohnaia and Mikiji Miyata*a
Received (in XXX, XXX) Xth XXXXXXXXX 20XX, Accepted Xth XXXXXXXXX 20XX
5
DOI: 10.1039/b000000x
groups in crystallography (Figure 1b(iv)). The X-Bs in the last
50 step plays a decisive role in determining the final crystal structure.
Bundling of the hydrogen bonded 2-fold helical columns has
been altered on the basis of a robust halogen bond between an
iodine and anionic oxygen atom. This alteration causes a
change of the space groups of the resulting crystals.
10 Helices are one of the most essential structural motifs in nature
and originate sophisticated functions of DNA and proteins. Even
artificial helices exhibit fascinating functions for asymmetric
catalysts, optoelectronics materials and so on. Such functions
motivate chemists to develop various helices in liquids, liquid
15 crystals and crystals.1 However, we usually face difficulties for
bundling the helices. For example, it still remains a challenge
whether we can design organic crystals with desired space groups
owing to the controlled bundling of helical motifs.
In the crystalline phase, organic molecules tend to construct
20 two-fold (21) helical assemblies due to dense packing and
cancelling of dipole moments.2 This tendency is strongly
supported by the fact that crystals involving 21 helices occupy
over seventy percent of the crystals registered on the Cambridge
Structural Database (CSD)3, including crystals with enantiopure
25 and racemic 21 helices belonging to chiral (ca. fifteen percent)
and achiral space groups (ca. fifty-five percent), respectively. For
the purpose of controlling the bundles, a useful tool may come
from supramolecular synthons which make characteristic
molecular
associations
through
various
non-covalent
30 interactions.4 Figure 1a shows three typical examples. Charge-
assisted hydrogen bonds (caH-Bs), CH-π bonds (CHπ-Bs) and
halogen bonds (X-Bs) afford the corresponding robust networks,5
herringbone associations of aromatic molecules,6 and halogen-
involved associations,7 respectively.
Figure 1. (a) Representative supramolecular synthons in organic
crystals: (i) charge-assisted hydrogen bonds (caH-Bs), (ii) CH-π
bonds (CHπ-Bs) and (iii) halogen bonds (X-Bs). (b) Hierarchical
55 construction of organic crystals on the basis of a "three-stepwise
and three-directional associations" method. (i) Construction of 1-
D 21 helices by caH-Bs, (ii) bundling of the helices in 2-D sheet
motifs by inter-columnar CHπ-Bs and (iii) piling of the sheet
motifs by inter-columnar X-Bs (iv) in 3-D crystals with specific
60 space groups. Green, blue and red balls exhibit halogen atoms, a
chiral primary amine (1) and p-halo-substituted achiral benzoic
acid derivatives (2), respectively. Green, light blue and black
dotted lines exhibit X-Bs, caH-Bs and CHπ-Bs, respectively.
35
This article deals with an effective use of the X-Bs for
bundling the 21 helical columns. As far as we know, there is no
research for selectively bundling the columns with the aid of the
X-Bs. For design of the crystals we propose a method, termed as
three-stepwise and three-directional associations, which is based
40 on the bundling with three kinds of the supramolecular synthons.
Figure 1b exemplifies the method. Firstly, the one-dimensional
(1-D) 21-helical columns of supramolecular building blocks are
constructed with the caH-Bs along a vertical direction (Figure
1b(i)). Secondly, the columns are combined with the inter-
45 columnar CHπ-Bs along a front-back direction to provide a 2-D
sheet motif (Figure 1b(ii)). Thirdly, the motifs are piled with the
inter-columnar halogen bonds (X-Bs) along a horizontal direction
(Figure 1b(iii)), yielding 3-D crystals which belong to any space
Regarding the building blocks, we focused on the chiral
65 columns of organic salts composed of an aromatic amine and
carboxylic acid (Figure 1b(i)). This is because the chiral salts
form definite right- or left-handed 21 helical columns with the
caH-Bs.8 Additional aromatic rings associate in a herringbone
manner with the CHπ-Bs so as to bundle the 21 helices. This
70 combination of the caH-Bs and CHπ-Bs enabled us to examine an
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effect of the inter-columnar X-Bs on the bundling. Taking into
account these considerations, we employed the X-Bs of a series
of halogen atoms attached at p-positions of benzoic acids. Their
of 1·2-I has I···O type of the X-Bs with a distance of 3.04 Å. This
difference can be explained by the three-stepwise and three-
directional association method as mentioned below. As for 2-F,
inter-columnar X-Bs would work for the control of the columnar 45 2-Cl and 2-Br, the 1-D columns are connected through the inter-
5
bundles. Plausible bundle manners of the chiral columns are as
follows; a parallel fashion with an inter-columnar two-fold
rotation axis, parallel or anti-parallel fashions with an inter-
columnar 21 helical axis, which correspond to the space groups;
C2, P21 or P212121, respectively (Figure 1b(iv)).
Chiral salts, which are composed of (R)-1-(2-
naphthyl)ethylamine (1) and benzoic acid (2-H) or its p-halo-
substituted derivatives (2-F, 2-Cl, 2-Br, 2-I), were prepared by
mixing them in methanol with a 1:1 molar ratio. Evaporation of
columnar CHπ-Bs, producing the herringbone associations
between the benzene and naphthalene rings in a parallel fashion
along the crystallographic c axis (Figure 2c(i)). This bundling
results in the 2-D sheet motifs spreading on the bc plane. The
50 third step is that the sheet motifs pile up in a parallel fashion
along the a axis through fits of asperities with the subsidiary
inter-columnar X-Bs (Figure S2 and Table S1), yielding the 3-D
crystals with the space group C2 (Figure 2d(i)). On the other hand,
the second step of 1·2-I consists of the herringbone associations
10
the solution yielded their powdered salts. Their single crystals 55 between the naphthalene rings in a parallel fashion, resulting in
15 were obtained by recrystallization of the salts from ethanol.
Crystallographic studies revealed that the crystals of 2-H, 2-F, 2-
Cl, 2-Br belong to the space groups C2 while the crystal of 2-I
does to the P212121 (Table 1 and Figure S1). The resulting
regulation of the bundles can be explained below.
the zigzag sheet motif on the ab plane (Figure 2c(ii)). The third
step is that the 2-D sheet motifs pile up in an anti-parallel fashion
along the c axis through the I···O type of the X-Bs, yielding the 3-
D crystals with the space group P212121 (Figure 2d(ii)).
60
Such a regulation of the bundling manners is clearly
20
Figure 2a shows formation of almost the same columns in
shape, which is confirmed by small differences of their helical
pitches (p) and length of the caH-Bs (d1, d2, d3) (Figure 2b and
Table 1). The hydrogen bonded ···N···O···N···O··· linkages
attributable to the strength of the X-Bs. The theoretical study
clarifies that the interaction energy originates from negative
electrostatic potential around halogen atoms and positive
potential on the center of the C‒X axis denoted as "σ-hole", and
consist of the left-handed 21 helices, which are denoted by supM, 65 increase in the order; F < Cl < Br < I.10 Especially, iodide has the
25 according to the supramolecular-tilt-chirality method (Figure 2b,
Figure S1a).8,9 The columns are stabilized by the intra-columnar
CHπ-Bs which provide herringbone associations between the
benzene and naphthalene rings. The CHπ-Bs have distances of
largest positive potential on its σ-hole region, and therefore
preferentially interacts with anions. Actually, I···O type X-Bs (d
= 3.04 Å) is observed in the P212121 crystal, where the iodide
atom is located on the major axis and the anionic oxygen atom is
2.6 to 3.1 Å between a hydrogen atom of the benzene or 70 on the center of the minor axis in the column (Figure 2b(i)). Such
30 naphthalene ring and a π-plane of the other neighbour ring.
a position causes the zigzag bundle of the columns, leading to
generation of different 21 helical axes which are perpendicular to
those of the 21 hydrogen bonded helices. As a result, the crystal
belongs to the space group P212121 with the helical axes along
75 three axes, a, b and c.
Table 1. Crystal parameters of 1·2-H to 1·2-I
Entries SGa SMC b p (Å)c d1, d2, d3 (Å)d dx-x (Å)e
d1: 2.794
1·2-H
1·2-F
C2
C2
C2
C2
supM 6.200
supM 6.217
supM 6.196
supM 6.195
-
In order to confirm the strength of the I···O type X-B, ab initio
calculation (MP2/6-311G**) was conducted (Figure S3 and Table
S2).11,12 Carboxylate anions (A to D) and amino cations (E to H)
have negative and positive charges, respectively. The charges
80 cause strong repulsive forces between the anions (B-D) or the
cations (E-F), as well as strong attractive forces between the
cation and the anion (A-E and B-E, Figure S3a). It is difficult
under this ionic condition to discuss the energy of X-Bs, which
localizes and have much smaller interaction energies than that
85 between ionic molecules, on the basis of calculation on whole
interaction energies among the ions. For getting over the problem,
the anionic carboxylate group of the molecule D was replaced by
hydrogen atom to neutralize, resulting in neutral molecule D'
(Figure S3b). The calculated energy of the I···O type of the X-B
90 (B-D') is -5.0 kcal/mol which is comparable to hydrogen bonds
of water molecules. This result suggests that the I···O type X-B
acts preferentially for the bundling of the columns in the crystal.
In conclusion, we have demonstrated the fusion method for
obtaining organic crystals on the basis of the bundling of the 21
95 helical columns through supramolecular synthons such as caH-Bs,
CHπ-Bs and X-Bs. The X-Bs are effective for controlling
bundling manners of the columns, leading to the selective
acquisition of the C2 and P212121 crystals with a parallel and
zigzag bundling manners, respectively. The I···O type of the X-
d2: 2.777
d3: 2.758
d1: 2.801
d2: 2.754
d3: 2.762
d1: 2.809
d2: 2.771
d3: 2.757
d1: 2.811
d2: 2.769
d3: 2.751
d1: 2.763
d2: 2.761
d3: 2.734
3.516
3.574
3.819
1·2-Cl
1·2-Br
5.691
1·2-I P212121 supM 5.961
(3.038)f
aSpace groups of the resulting crystals. Supramolecular chirality
b
c
of the caH-Bs. Pitches of the 21 helical columns with caH-Bs.
dLength of the caH-Bs in the columns as distance of O···N.
35 eDistances between the closest halogen atoms. Length of I···O
f
type X-Bs.
Subsequently, the columns are connected by the inter-
columnar CHπ-Bs and X-Bs (Figure 2c), yielding different
crystal structures (Figure 2d). Table 1 shows that C2 crystals of
40 1·2-F, 1·2-Cl and 1·2-Br have the X-Bs such as F···F, Cl···Cl and
Br···Br with distances of 3.52 to 3.82 Å, while the P212121 crystal
2
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Figure 2. Crystal structures of the chiral salts. (a) The 1-D 21 helical hydrogen bonded columns of (i) 1•2-H, (ii) 1•2-F, 2-Cl, 2-Br
(superimposed) and (iii) 1•2-I drawn with thermal ellipsoid with 50% probability. (b) Schematic representation of the column. (c) The
bundling of the columns through the CHπ-Bs and X-Bs for 1•2-H, -F, -Cl, -Br (i) and 1•2-I (ii). (d) The crystals with the space group C2
involving X···X type of the X-Bs. (i) and P212121 involving I···O type of the X-Bs (ii). Their packing diagram are drawn with unit cells and
symmetry symbols, which include our proposed symbols representing right- and left-handed 21 helices.9 Amplifications around the X-Bs in
the crystals were exhibited in insertion boxes.
hisaki@mls.eng.osaka-u.ac.jp, miyata@mls.eng.osaka-u.ac.jp
Bs provides a directional and robust association between the
molecules so as to yield the zigzag-type bundles.
This kind of research will contribute to set up a new and useful
b National Institute of Advanced Industrial Science and Technology
(AIST), Tsukuba, Ibaraki, 305-8568, Japan. Fax: (+)81-29-851-5426;
20 Tel: (+)81-29-851-5426; E-mail: s.tsuzuki@aist.go.jp
strategy for designing functional crystals as aggregates of the 21
helical columns. Further study has been going on to clarify the
effects of the X-Bs as well as the other functional groups on the
bundling of the columns.
This work was financially supported by KAKENHI (21245035,
24108723, 24350072 and 24651117) from MEXT (Japan). We
10 are grateful to Dr. K. Miura, Dr. S. Baba, and Dr. N. Mizuno for
their helpful discussion (proposal No. 2012A1570) in the SPring-
8, JASRI.
† Electronic Supplementary Information (ESI) available: Detailed
experimental procedure, theoretical calculation and crystallographic data.
CCDC 884890-884894. See DOI: 10.1039/b000000x/
5
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