Halogen bonding synthon modularity in coordination compounds

Article abstract of DOI:10.1021/acs.cgd.5b00282

In this Communication, the modulation of halogen bonding synthons in the crystal structure of [HgBr₂(L^3,4-diCl)] from [HgBr₂(L^3-Cl)] and [HgBr₂(L^4-Cl)], as single components, where L is a N

Full text of DOI:10.1021/acs.cgd.5b00282

Communication
pubs.acs.org/crystal
Halogen Bonding Synthon Modularity in Coordination Compounds
Hamid Reza Khavasi,* Fataneh Norouzi, and Alireza Azhdari Tehrani
Faculty of Chemistry, Shahid Beheshti University, G. C., Evin, Tehran 1983963113, Iran
S
* Supporting Information
ABSTRACT: In this Communication, the modulation of halogen bonding synthons in the crystal structure of [HgBr2(L3,4‑diCl)]
from [HgBr2(L3‑Cl)] and [HgBr2(L4‑Cl)], as single components, where L is a N-(chlorinatedphenyl)-2-pyrazinecarboxamide
ligand, has been investigated. Reviewing the crystal packing reveals that Cl···N and Cl···Br halogen bonds stood as a
remembrance of the crystal structures of single components in the packing of [HgBr2(L3,4‑diCl)].
he overall ambition of crystal engineering is the synthesis
zene has recently been reported.12 In 2011, the structural
Tof designed crystalline molecular structures with desired modularity in 2,3,4- and 3,4,5-trichlorophenol was reported by
Mukherjee and Desiraju.7 Inspection of the crystal packing
showed that the crystal structure of these chlorinated phenols
contains Cl···Cl interaction and hydrogen bonding patterns that
occur in the structures of monochlorophenol and dichlor-
ophenol. In spite of these reports on modularity in the crystal
structures of individual molecules, including chlorinated
phenols, and co-crystals of organic compounds,7−9,11 to the
best of our knowledge, the study of the synthon modularity in
the crystal structure of coordination compounds has not been
thoroughly discussed. As part of our effort for the investigation
of the effect of the weak intermolecular interactions in the
crystal packing of mercury coordination compounds including
pyrazine/pyridine carboxamide ligands,13−17 halogen bonding
synthon modularity in coordination compounds has herein
been reported for the first time. In the present study, three N-
properties.1−4 In this regard, a molecular structure can be
defined as a multisegment subject, where each segment, as a
single molecular component, carries one or more functional
groups, and so its crystal packing is involved in one or more
intermolecular synthon. Synthon modularity5−7 is the presence
of synthon repetitivity between functional groups of a
molecular structure and functional groups of its segments.
Since the final crystal packing may be defined based on the
gathering of different synthons from different segments,
synthon modularity is rare and there are limited examples
reported in the literature. In a recent paper by Desiraju,8 co-
crystals of 4-hydroxybenzamide with aliphatic dicarboxylic acids
based on strong hydrogen bonding synthon modularity have
been reported. The modulation of O−H···N synthons in the
systematic cocrystallization of mono-, di-, and trihydroxyben-
zoic acids with hexamine was investigated by Guru Row and co-
workers in 2014.9 In contrast to the presence of different
interactions in the formation of co-crystals, reports on synthon
modularity in cocrystals based on halogen bond interactions10
are rare. Desiraju and his co-workers also described the design
of binary11 and ternary12 co-crystals based on hydrogen bond
and halogen bond synthon modularity. The crystal packing of
4-bromobenzamide-n-alkyldicarboxylic acid co-crystals, shows
that O−H···O hydrogen bonds are reminiscence of the crystal
structure of dicarboxylic acid while type I and type II Br···Br
interactions are similar to the crystal structure of 4-
bromobenzamide. Furthermore, the modulation of the O−
H···O hydrogen bonds and Br/I···O2N halogen bonds in
ternary co-crystals of 4-benzamide-dicarboxylic acid-dinitroben-
(chlorinatedphenyl)-2-pyrazinecarboxamide ligands, L3‑Cl, L4‑Cl
,
and L3,4‑diCl (Scheme 1), carrying chlorine atoms in phenyl
meta- or/and para-positions, have been employed for the
synthesis of mercury(II) bromide complexes. Examining the
crystal packing of [HgBr2(L3,4‑diCl)] clearly shows that the Cl···
N and Cl···Br halogen bonding synthons are a remembrance of
the crystal structures of [HgBr2(L3‑Cl)] and [HgBr2(L4‑Cl)],
respectively, as single components. It should be noted that
complex 1 has been previously reported by some of us,16 but
here, we present a comparative study of this crystal structure
Received: February 26, 2015
Revised: April 19, 2015
© XXXX American Chemical Society
A
DOI: 10.1021/acs.cgd.5b00282
Cryst. Growth Des. XXXX, XXX, XXX−XXX

Crystal Growth & Design
Communication
Scheme 1. Synthesized Complexes [HgBr2(L3‑Cl)], 1,
[HgBr2(L4‑Cl)], 2, and [HgBr2(L3,4‑diCl)], 3
with the other two new structures, complexes 2 and 3, for
studying the synthon modularity. Our opinion is that the results
of the present study can be helpful in crystal engineering
especially in the crystal structure prediction research field.
The ligands, L3‑Cl, L4‑Cl, L3,4‑diCl, were synthesized by the
reaction of 3-chloroaniline, 4-chloroaniline, or 3,4-dichloroani-
line and pyrazinecarboxylic acid in 1:1 ratio and in the presence
of triphenyl phosphite (for details of the experimental
procedures, see the Supporting Information).18,19 A reaction
between methanolic solutions of HgBr2 and these ligands in 1:1
ratio afforded air-stable plate, prism, and block crystals of
[HgBr2(L3‑Cl)], 1, [HgBr2(L4‑Cl)], 2, and [HgBr2(L3,4‑diCl)], 3,
respectively, after a few days. A summary of the crystallographic
data and structure refinement is listed in Table S1. Selected
lengths and angles with estimated deviations are summarized in
Table S2. X-ray diffraction analysis ascertains that all complexes
crystallized in orthorhombic crystal system with space group of
Cmca for 1 and 3 and Pbca for 2 (Table S1). The asymmetric
unit of these compounds comprises two bromine atoms, one
Hg2+ ion, and one crystallographically independent ligand.
ORTEP drawings with the atom labeling schemes used for
compounds 2 and 3 are shown in Figure S1. In all three
structures, the central metal atom is three-coordinated and lies
in a T-shaped geometry formed by one pyrazine nitrogen atom
of ligand and two bromine atoms. These compounds have a
trigonal-planar index, τ3,16 of 0.32, 0.21, and 0.23, respectively.
Inspection of the crystal structure of these compounds reveals
that the packing difference between them can be discussed by
considering intermolecular interactions in the b-direction. In
complex 1, individual molecules form a linear chain in the b-
direction by Cl···N halogen bonds (Figure 1 (up) and Table 1).
The Cl···N distance is 3.217(5) Å, and so is 2.5% shorter than
the sum of van der Waals radii of chlorine and nitrogen
atoms.20 The angle of C−Cl···N is 163.5 (5)° which is in
accordance with n(nitrogen) → σ*(chlorine) electron donation.21
These halogen bonds are accompanied by the weak hydrogen
bonds between the C−H donor and the carbonyl oxygen
acceptor (Figure 1 (up) and Table 1). In complex 2, individual
units are closely packed through C−Cl···Br−Hg contacts
(Figure 1 (down), Table 1) to generate a 1D chain in the b-
direction. The distance of Cl···Br contacts was found to be
about 3.548(4) Å, which is 1.4% shorter than the sum of the
van der Waals radii of chlorine and bromine atoms.20 There are
also C−H···Cl weak hydrogen bonds that cooperate in the
Figure 1. Side view representation of complexes 1−3 in a-direction,
illustrating the presence of Cl···N halogen bonds, XBClN synthon (red-
highlighted) in 1, (up), the presence of Cl···Br halogen bonds; XBClBr
synthon (green-highlighted) in 2, (down), and modulation of both
halogen bonds in 3, (middle).
halogen bonding interactions (Table S3). In complex 3, in the
b-direction, there are two different halogen bonding synthons,
XBClN, Cl···N, and XBClBr, Cl···Br. The distance of XBClN and
XBClBr contacts was found to be about 2.967(6) and 3.477(5)
Å, respectively, which is 10.1% and 3.4% shorter than the sum
of the van der Waals radii of chlorine and nitrogen/bromine
atoms20 (Table 1). In this complex, adjacent molecules are
linked to each other through these XB synthons with the
cooperation of N−H···Cl and C−H···OC hydrogen bonds,
to generate linear chains in the b-direction, similar to complexes
1 and 2 (Figure 1 (middle), Table S3). As indicated in Figure 1,
synthon XBClN is reminiscent the crystal packing of 2, while
synthon XBClBr is modulated from 2 to 3. Therefore, the meta-
chloro and para-chloro positions in 3 play the same roles as
they do in 1 and 2, individually. These structural correlations
B
DOI: 10.1021/acs.cgd.5b00282
Cryst. Growth Des. XXXX, XXX, XXX−XXX

Crystal Growth & Design
Communication
Table 1. Halogen Bond Parameters and Calculated Binding
Energies for Complexes 1−3
a
complex
1
2
3
c
c
e
Cl···N (Å)
Cl···Br (Å)
C−Cl···N (deg)
C−Cl···Br (deg)
Hg−Br···Cl (deg)
Reduction of the sum of
the vdW radii (%)
3.217(5)
-
-
2.967(6)
3.477(5)
d
3.548(5)
-
163.5(5)
179.4(6)
-
122.1(5)
130.7(6)
166.2(5)
10.1, 3.4
Figure 3. Asymmetric units of compounds 1 (green), 2 (violet), and 3
(red) superimposed to illustrate the conformational freedom of the
flexible carboxamide ligand.
-
169.7(1)
1.4
f
2.5
b
Binding energy (kJ/mol)
a
−31.10
−30.53
−36.70
b
From ref 16. The values are related to the energy of the interaction
same conformation. Moreover, in all three complexes pyrazine
and phenyl rings are in-plane with the maximum deviation of
less than 9° for complex 2. These structural similarities can
reinforce the modulation of different synthons of 1 and 2 into
the structural packing of 3.
c
d
between two adjacent fragments (Figure S2). 1−x, 1/2+y, 1/2−z. −
x, −1/2+y, 1/2−z. 1−x, −1/2+y, 1/2−z. These values are related to
Cl···N and Cl···Br halogen bonds, respectively.
e
f
provide a unique example of the structural modularity in
coordination compounds based on halogen bonding inter-
actions. In these complexes, linear chains are linked together
through head-to-tail πphen···−NHCO− interactions in a-
direction to generate 2D sheets (Figure 2, Table S3). In the
packing of these complexes, the overall supramolecular
assemblies result from the linkage of 2D sheets by Hg···Br
contacts (Figure 2, Table S3). The Hg···Br contacts of
3.401(1), 3.367(5), and 3.414(6) Å for 1−3, respectively, are
comparable to those previously reported.16,22 Conformational
adaptation of the ligands for the generation of different
conformers in the packing of crystals 1−3, is allowed due to the
flexibility of the chlorinated ligands for rotation around the
Cpyz-CONamide bonds. This flexibility has been shown in our
previous reports for similar carboxamide ligands.13,16,23,24 As
indicated in Figure 3, which shows the HgBr2−Pyz-super-
imposed units of complexes 1−3, all three ligands have the
Qualitative support for this similarity is afforded by
comparing the electrostatic potential maps for compounds
1−3 (Figure 4). These electrostatic potential maps show that,
although the presence of two chlorine atoms on the aromatic
ring causes complex 3 to essentially have lower negative
electrostatic potentials above and below the phenyl ring,
compared to 1 and 2, according to the side view representation
of the halogen σ-hole, shown on the right side of each MEP, it
can be concluded that chlorine atoms in both meta and para
positions have nearly the same participation in the halogen
bonding interaction. These intermolecular interactions can also
be quantified via Hirshfeld surface analysis study. The
contributions of Hg···Br, π···amide, Cl···N, and Cl···Br contacts
to the Hirshfeld surface areas are illustrated in Figure 5. As
clearly shown by this histogram, Hg···Br and π···amide contacts
have nearly the same contribution in all complexes. In complex
1, the Cl···N halogen bond contributes by 1.4%. From 1 to 2,
Figure 2. Generation of 2D sheets through head-to-tail πphen···(NHCO) interactions (pink ribbon) in a-direction and formation of overall
supramolecular assemblies from the linkage of 2D sheets by Hg···Br contacts (gray ribbon) in complex 1, left side, and complex 3, right side.
Different colors show different adjacent linear chains. XBClBr and XBClN synthons are red- and green-highlighted, respectively.
C
DOI: 10.1021/acs.cgd.5b00282
Cryst. Growth Des. XXXX, XXX, XXX−XXX

Crystal Growth & Design
Communication
involved in the Cl···Br halogen bond with a contribution of
5.6%. In complex 3, the contribution of both XB contacts, 4.4%
and 5.7% for Cl···N and Cl···Br, respectively, was observed.
Furthermore, the evaluation of these halogen bonding
interactions involving synthon modularity can be done by
DFT-calculation of the binding energies between two relative
fragments. Theoretical calculations were achieved at the LDA-
ZORA- TZP level on fragments directly cut out from the
experimental data. Calculated binding energies are listed in
Table 1. This data shows that binding energies between two
adjacent fragments involving halogen bonding interactions
ranges from −30.53 to −36.70 kJ mol−1. Based on strength and
directionality, it can be concluded that these halogen bonds,
XBClN and XBClBr, play an important role in determining the
final supramolecular structures.
In conclusion, modulation of halogen bonding synthons in
the crystal structures of HgBr2 complexes of N-(chlorinated-
phenyl)-2-pyrazinecarboxamide ligands have been investigated.
Results clearly show that in the crystal packing of
[HgBr2(L3,4‑diCl)], the Cl···N and Cl···Br halogen bonds are
reminiscent of the crystal packing of [HgBr2(L3‑Cl)] and
[HgBr2(L4‑Cl)], respectively, as single components. This study
is the first report on structural modularity in coordination
compounds, and can be useful in different branches of inorganic
crystal engineering such as polymorphism and crystal structure
prediction.
Figure 4. Electrostatic potentials mapped on the electron isodensity
surface of 1 (a), 2 (b), and 3 (c) at the same contour value of 0.008
electron per Bohr.3 Areas of high electron density are shown as red
and low electron density as blue. The side view representation of
chlorine σ-hole is shown on the right side of each electrostatic
potentials map.
ASSOCIATED CONTENT
* Supporting Information
■
S
Experimental details, the ORTEP diagram, fragments selected
for calculation of dimer binding energies, crystallographic data,
selected bond distances and bond angles, and intermolecular
interaction parameters. The Supporting Information is available
free of charge on the ACS Publications website at DOI:
10.1021/acs.cgd.5b00282.
AUTHOR INFORMATION
Corresponding Author
*E-mail: h-khavasi@sbu.ac.ir.
■
Notes
The authors declare no competing financial interest.
ACKNOWLEDGMENTS
■
We would like to thank Graduate Study Councils of Shahid
Beheshti University, General Campus for financial support.
REFERENCES
■
(1) Desiraju, G. R. Crystal Engineering. The Design of Organic Solids;
Elsevier: Amsterdam, 1989.
(2) Grepioni, F.; Braga, D. Making Crystals by Design-From Molecules
to Molecular Materials, Methods, Techniques, Applications; Wiley-VCH:
Weinheim, Germany, 2007.
(3) Desiraju, G. R. The Crystal as a Supramolecular Entity; John Wiley
& Sons: New York, 1996.
(4) Steed, J. W.; Atwood, J. L. Supramolecular Chemistry; Wiley:
Chichester, 2000.
Figure 5. Selected contribution percentages of Hg···Br, π···amide, Cl···
N, and Cl···Br contacts in the crystal packing of complexes 1−3. π···
amide considered as the sum of C···N and C···O contacts. Data for
complex 1, is calculated using CIF file with CSD entry code of
QEZPOC, reported in ref 16.
(5) Desiraju, G. R. J. Am. Chem. Soc. 2013, 135, 9952−9967.
(6) Mukherjee, A.; Tothadi, S.; Desiraju, G. R. Acc. Chem. Res. 2014,
47, 2514−2524.
(7) Mukherjee, A.; Desiraju, G. R. Cryst. Growth Des. 2011, 11,
3735−3739.
by changing the chloro-position, the contribution of the Cl···N
halogen bonds decreased to 0.0%, and the chlorine atom was
(8) Tothadi, S.; Desiraju, G. R. Cryst. Growth Des. 2012, 12, 6188−
6198.
D
DOI: 10.1021/acs.cgd.5b00282
Cryst. Growth Des. XXXX, XXX, XXX−XXX

Crystal Growth & Design
Communication
(9) Kaur, R.; Lalithalakshmi, B. V.; Guru Row, T. N. Cryst. Growth
Des. 2014, 14, 2614−2620.
(10) Desiraju, G. R.; Ho, P. S.; Kloo, L.; Legon, A. C.; Marquardt, R.;
Metrangolo, P.; Politzer, P.; Resnati, G.; Rissanen, K. Pure Appl. Chem.
2013, 85, 1711−1713.
(11) Tothadi, S.; Joseph, S.; Desiraju, G. R. Cryst. Growth Des. 2013,
13, 3242−3254.
(12) Tothadi, S.; Sanphui, P.; Desiraju, G. R. Cryst. Growth Des. 2014,
14, 5293−5302.
(13) Khavasi, H. R.; Esmaeili, M. CrystEngComm 2014, 16, 8479−
8485.
(14) Khavasi, H. R.; Mir Mohammad Sadegh, B. Dalton Trans. 2014,
43, 5564−5573.
(15) Khavasi, H. R.; Azhdari Tehrani, A. CrystEngComm 2013, 15,
5799−5812.
(16) Khavasi, H. R.; Azhdari Tehrani, A. Inorg. Chem. 2013, 52,
2891−2905.
(17) Khavasi, H. R.; Azizpoor Fard, M. Cryst. Growth Des. 2010, 10,
1892−1896.
(18) Sasan, K.; Khavasi, H. R.; Davari, M. D. Monatsh. Chem. 2008,
139, 773−780.
(19) Khavasi, H. R.; Azhdari Tehrani, A. CrystEngComm 2013, 15,
3222−3235.
(20) Bondi, A. J. Phys. Chem. 1964, 68, 441−451.
(21) Ananthavel, S. P.; Manoharan, M. Chem. Phys. 2001, 269, 49−
57.
(22) Wu, J.-Y.; Hsu, H.-Y.; Chan, C.-C.; Wen, Y.-S.; Tsai, C.; Lu, K.-
L. Cryst. Growth Des. 2009, 9, 258−262.
(23) Khavasi, H. R.; Ghanbarpour, A.; Azhdari Tehrani, A.
CrystEngComm 2014, 16, 749−752.
(24) Khavasi, H. R.; Azhdari Tehrani, A. CrystEngComm 2013, 15,
5813−5820.
E
DOI: 10.1021/acs.cgd.5b00282
Cryst. Growth Des. XXXX, XXX, XXX−XXX