Directionality and site selectivity of N?Cl halogen bonding in two azaaromatic chloride crystals

Article abstract of DOI:10.1016/j.molstruc.2010.04.035

Two azaaromatic chlorides of bis-2,4-[(2-formoyl)phenoxyl]-6-chloro-[1,3,5]triazine (1) and bis-2,4-(4-carbomethoxyphenoxyl)-6-chloro-[1,3,5]triazine (2) have been synthesized and structurally characterized. The crystal structures of 1 and 2 reveal unusually short intermolecular N?Cl distance of 3.095(2) and 3.088(3) ?, meaning the formation of strong halogen bonding. The strengths of the intermolecular N?Cl halogen bonding and the molecular electrostatic potentials in these crystal structures have been calculated by Density Functional Theory Calculations. The capacities of the N?Cl halogen bonding, lone pair?π interaction, π-π stack and C-H?O hydrogen bonding in the directionality of supramolecular self-assembly have been analyzed by structural study and theoretical calculations. The site selectivity of the N?Cl halogen bonding is illustrated by the difference of electrostatic potential of the N atoms on the molecule.

Full text of DOI:10.1016/j.molstruc.2010.04.035

Journal of Molecular Structure 975 (2010) 274–279
Contents lists available at ScienceDirect
Journal of Molecular Structure
journal homepage: www.elsevier.com/locate/molstruc
Directionality and site selectivity of NÁ Á ÁCl halogen bonding in two
azaaromatic chloride crystals
a
a
c
Yi-Min Zhu a, Ti-Fang Miao a,b, Yang-Yi Yang a, , Dong-Yue Zhuang , Kang-Cheng Zheng , Wing-Tak Wong
*
a MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry and Chemical Engineering, Sun Yat-Sen University, Guangzhou 510275, PR China
b College of Chemistry and Materials Science, Huaibei Normal University, Huaibei 235000, PR China
c Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, PR China
a r t i c l e i n f o
a b s t r a c t
Article history:
Received 9 March 2010
Received in revised form 23 April 2010
Accepted 23 April 2010
Available online 29 April 2010
Two azaaromatic chlorides of bis-2,4-[(2-formoyl)phenoxyl]-6-chloro-[1,3,5]triazine (1) and bis-2,4-(4-
carbomethoxyphenoxyl)-6-chloro-[1,3,5]triazine (2) have been synthesized and structurally character-
ized. The crystal structures of 1 and 2 reveal unusually short intermolecular NÁ Á ÁCl distance of
3.095(2) and 3.088(3) Å, meaning the formation of strong halogen bonding. The strengths of the intermo-
lecular NÁ Á ÁCl halogen bonding and the molecular electrostatic potentials in these crystal structures have
been calculated by Density Functional Theory Calculations. The capacities of the NÁ Á ÁCl halogen bonding,
Keywords:
Halogen bonding
Directionality
Site selectivity
DFT calculations
Molecular electrostatic potential
lone pairÁ Á Á
p
interaction,
p
–
p
stack and CÀHÁ Á ÁO hydrogen bonding in the directionality of supramolec-
ular self-assembly have been analyzed by structural study and theoretical calculations. The site selectiv-
ity of the NÁ Á ÁCl halogen bonding is illustrated by the difference of electrostatic potential of the N atoms
on the molecule.
Ó 2010 Elsevier B.V. All rights reserved.
1. Introduction
halogen bonding, we herein report the synthesis and crystal struc-
ture of two new azaaromatic chlorides (Scheme 1), bis-2,4-[(2-for-
Intermolecular interactions play crucial roles in supramolecular
chemistry [1] and crystal engineering [2]. Among these interac-
moyl)phenoxyl]-6-chloro-[1,3,5]triazine (1) and bis-2,4-(4-
carbomethoxyphenoxyl)-6-chloro-[1,3,5]triazine (2). The designs
of the molecular structures 1 and 2 are based on the following con-
siderations. First, azaaromatic chlorides may form short NÁ Á ÁCl con-
tact in their solid state [36], which means the formation of strong
halogen bonds [28]. Second, if a molecule has more than one N
atom, it is possible that only some of them are involved in the for-
mation of halogen bonding, which is a site-selective supramolecu-
tions, hydrogen bonding and
important ones [3,4]. Very recently, a new kind of supramolecular
interaction, has been consid-
p–p stack are probably the most
interaction, namely the lone pairÁ Á Á
p
ered to construct supramolecular framework [5], that is a type of
noncovalent interaction between atoms that contain lone pair elec-
tron and electron-deficient
p-ring [6]. Halogen bonding is also a
‘‘new” intermolecular interaction [7] that has attracted great inter-
est in recent years [2,3,8–22]. It is an analogue of hydrogen bond-
ing and is also used in crystal engineering to construct a variety of
architectures [23–27]. The remarkable strength of some halogen
bondings enable them to prevail over hydrogen bondings in the
construction of crystal structures [28].
lar synthesis [11]. Third, the lone pairÁ Á Á
p interaction between
carbonyl group and electron-deficient triazine ring could be used
to assemble supramolecules [5].
An analysis of the crystal structures 1 and 2 reveals that
N(sp2)Á Á ÁCl halogen bonding not only exists in the two crystal
structures but also dominates the direction of self-assembly of
the supramolecules. The formation of the N(sp2)Á Á ÁCl halogen
bonding in these crystal structures is site-selective, as only the N
atoms opposing to the CÀCl bonds (the opposing N atoms) on
the molecules 1 and 2 are involved in the formation of the halogen
bonding. In other words, the Cl atoms on the molecules 1 and 2
We are interested in searching for new intermolecular interac-
tions to assemble supramolecules with novel structures [4,29–35].
The emergence of halogen bonding and lone pairÁ Á Á
p interactions
in recent years has motivated us to study their roles in the assem-
bly of supramolecules. To evaluate the directional capacities of the
N(sp2)Á Á ÁCl halogen bonding, lone pairÁ Á Á
p
interaction, CÀHÁ Á ÁO
recognize the opposing N atoms. The lone pairÁ Á Á
p interactions
hydrogen bonding and p–p stack in the construction of supramol-
exist in the crystal structure of 1. It is seldom reported that lone
ecules and to investigate the site selectivity of the N(sp2)Á Á ÁCl
pairÁ Á Á
p
interactions and NÁ Á ÁCl halogen bonding take part in the
assembly of supramolecules simultaneously.
To estimate quantitatively the capacity of halogen bonding, lone
* Corresponding author. Tel.: +86 20 84112977.
E-mail address: cesyyy@mail.sysu.edu.cn (Y.-Y. Yang).
pairÁ Á Á
p
interaction,
p–p
stack and CÀHÁ Á ÁO hydrogen bonding in
0022-2860/$ - see front matter Ó 2010 Elsevier B.V. All rights reserved.
doi:10.1016/j.molstruc.2010.04.035

Y.-M. Zhu et al. / Journal of Molecular Structure 975 (2010) 274–279
275
was cooled to 0 °C. Methyl p-hydroxybenzoate (20 mmol) was
added portionwise. After the completion of the addition, the sus-
pension mixture was warmed to room temperature and then
heated at 50 °C for 6 h. The mixture was filtered and the solvent
of the filtrate was evaporated under reduced pressure to give the
crude product, which was recrystallized from THF to give the white
powder 2. Yield 2.41 g (49.4%); m.p. 201–202 °C. Anal. Calc. For
C
23H22ClN3O7 (2): C, 56.6; H, 4.5; N, 8.6; Found: C, 56.4; H, 4.4;
N, 8.9%. FT-IR (KBr, cmÀ1): 3007, 2957, 2848, 1723, 1561, 1529,
1365, 1283, 1242, 948, 773, 703.
2.2. X-ray crystallographic study
Colorless block crystals of 1 were grown from acetone in one
week. Colorless plate crystals of 2 were grown from THF in a few
days.
X-ray data were collected on a Bruker SMART 1000 CCD diffrac-
tometer, Mo
T = 173(2) K (for 1) and on an Oxford Gemini S Ultra diffractometer,
Mo K (k = 0.71073 Å), graphite monochromator at T = 150(2) K
Ka (k = 0.71073 Å), graphite monochromator at
Scheme 1. Line drawings of the compounds 1 and 2.
the direction of self-assembly of supramolecules, we calculated the
strengths of the halogen bonding in these crystal structures, and
compared the results with the strengths of the other three intermo-
lecular interactions. We also calculated the molecular electrostatic
potentials of 1 and 2. The outcome may illustrate the site selectivity
between Cl atoms and different N electron-donor sites on the tri-
azine rings [13]. The results of the molecular electrostatic potential
calculations indicate that the opposing N atoms in 1 and 2 have more
abilitiesto interact with Cl atomsthrough theregions ofnegativepo-
tential ontheir surfaces. As a result, molecularelectrostaticpotential
calculations have significant contribution in the description of the
site selectivity between Cl atoms and different N electron-donor
sites on the triazine rings. Additionally, this kind of site selectivity
may partly contribute from the shape of the molecules, as suggested
by Báthori et al. [36]. To the best of our knowledge, there are no re-
ports on the study of the directionality of N(sp2)Á Á ÁCl halogen bond-
ing and site selectivity of halogen bonding by using a structural
method together with theoretical calculations.
a
(for 2). The initial structure models were obtained by direct meth-
ods [38] for 1 and by Patterson method [38] for 2 and subsequent
difference synthesis for both 1 and 2. H atoms were positioned
geometrically and allowed to ride on their parent atoms with
Uiso(H) = 1.2Ueq(C) for CH and CH2 groups and Uiso(H) = 1.5Ueq(C)
for CH3 group. The structures were refined by full-matrix least-
squares methods with SHELXL-97 module [39]. Crystallographic
data are listed in Table 1.
2.3. Theoretical methods
All the calculations were preformed by means of the Gauss-
ian03 program-package (revision D.01) [40]. All geometries were
optimized in vacuo using the restricted DFT-B3LYP method and
6-311GÃ basis set. Based on the optimized geometries, the molec-
ular electrostatic potentials were calculated at the same level of
theory. The energies of the halogen bonding were calculated with
2. Experimental
Table 1
Crystallographic data for 1 and 2.
2.1. Synthesis
1
2
Formula
Formula weight
Crystal system
Space group
Crystal size (mm)
a (Å)
C
17H10ClN3O4
C23H22ClNO7
487.89
Orthorhombic
Pnma
Both 1 and 2 were synthesized according to a literature proce-
dure [37] with minor modifications.
355.73
Monoclinic
C2/c
0.46 Â 0.41 Â 0.40
13.774(2)
7.460(1)
15.246(3)
99.489(3)
1545.2(4)
4
1.529
0.277
728
3.00–27.07
À17 6 h 6 13
À8 6 k 6 9
À17 6 l 6 19
4424
0.40 Â 0.38 Â 0.15
2.1.1. Synthesis of bis-2,4-[(2-formoyl)phenoxyl]-6-chloro-
[1,3,5]triazine (1)
7.4508(2)
b (Å)
c (Å)
25.690(1)
10.9543(4)
2,4,6-Trichloro-1,3,5-triazine (10 mmol) was dissolved in THF
(80 ml). Na3PO4 (20 mmol) was added and the suspension mixture
was cooled to 0 °C. Salicylaldehyde (20 mmol) was added portion-
wise. After the completion of the addition, the suspension mixture
was warmed to room temperature and then stirred at the same
temperature for 8 h. The resulting mixture was filtered. To the fil-
trate was added water (400 ml) portionwise leading to the forma-
tion of a white precipitate. The precipitate was collected by
filtration and washed with water (3 Â 20 ml) and recrystallized
from acetonitrile to give the white product 1. Yield 1.43 g
(40.2%); m.p. 207–208 °C. Anal. Calc. For C17H10ClN3O4 (1): C,
57.4; H, 2.8; N, 11.8; Found: C, 57.5; H, 3.0; N, 11.8%. FT-IR (KBr,
cmÀ1): 3082, 2765, 1698, 1606, 1560, 1358, 1273, 1234, 958, 770.
b (°)
V (Å3)
2096.8(1)
4
1.546
0.237
1016
3.31–27.99
À9 6 h 6 4
À33 6 k 6 29
À14 6 l 6 13
7096
Z
Dcalc (g/cm3)
l
(mmÀ1
)
F(0 0 0)
h ranges (°)
hkl range
Reflections collected
Independent reflections
Observed reflections (I > 2
Rint
1689
1473
0.0164
1.063
2758
1893
0.0274
1.057
r
(I))
Goodness-of-fit on F2
R(F) (I > 2
wR(F2) (I > 2
R(F) (all data)
wR(F2) (all data)
qmin (e ÅÀ3
r
(I))
0.0332
0.0938
0.0387
0.0987
0.0682
0.1918
0.0944
0.2047
r(I))
2.1.2. Synthesis of bis-2,4-(4-carbomethoxyphenoxyl)-6-chloro-
[1,3,5]triazine (2)
2,4,6-Trichloro-1,3,5-triazine (10 mmol) was dissolved in THF
(120 ml). K2CO3 (20 mmol) was added and the suspension mixture
D
qmax
,
D
)
0.339 and À0.160
1.205 and À0.789

276
Y.-M. Zhu et al. / Journal of Molecular Structure 975 (2010) 274–279
the DFT-B3LYP method and 6-311++GÃÃ basis set, using the same
optimized geometries as mentioned above. In addition, to accu-
rately obtain halogen bonding complexation energy, the basis set
superposition error (BSSE) was taken into account using the coun-
terpoise method [41].
lecular sheet (Fig. 2). The contact distances of the lone pairÁ Á Á
interaction are listed in Table 2. The two-dimensional sheets are
linked by stack between phenyl rings to form a three-dimen-
sional supramolecular array (Fig. 3). The centroid–centroid
distances within the stack are 3.8451(5) Å (measured in the
Diamond program).
p
p–p
In the molecular structure of 2, a mirror plane bisects the tri-
azine ring perpendicular to its plane across the CÀCl bond and
the opposing N atom (Fig. 4). The molecules of 2 also adopt the but-
terfly configuration similar to that of 1. Beside this, each molecule
of 2 in stacks is also halogen bonded to two adjacent molecules in a
head-to-tail mode, resulting in a one-dimensional chain (Fig. 5).
The intermolecular distance between the N and Cl atoms forming
the halogen bond is 3.088(3) Å and the angle of CÀClÁ Á ÁN is
177.6(2)°. However, the mode of packing of the one-dimensional
chains in the crystal structure of 2 is quite different from that of
1. In the crystal structure of 2, two adjacent one-dimensional
chains formed by halogen bonding connect with each other
through intermolecular CÀHÁ Á ÁO hydrogen bonding that is in-
volved in the methyl groups and the O atoms of the carbonyl
groups to form a double-chain motif (Fig. 5, Table 3). Numerous
double-chain motifs stack in a parallel mode to afford one-dimen-
sional channels along the crystallographic a axis (Fig. 6). Disor-
dered THF solvent molecules reside in these channels.
3. Results and discussion
In the molecular structure of 1, a twofold rotation axis passes
through the CÀCl bond and the opposing N atom (Fig. 1). The
two phenyl rings are almost perpendicular to the central triazine
ring with the dihedral angles of 99.7° (phenyl ring C3ÀC8) and
80.3° (phenyl ring C3AÀC8A), respectively. The two phenyl rings
are more tilted towards each other (dihedral angle: 53.1°). 1
adopts the butterfly conformation with two torsion angles
(N1ÀC2ÀO1ÀC3 and N1AÀC2AÀO1AÀC3A) of 1.2(2)° [42]. Fig. 2
shows that each butterfly-shaped molecule in the crystal structure
connects with two neighboring molecules in a head-to-tail mode
through intermolecular NÁ Á ÁCl halogen bonding, affording an infi-
nite one-dimensional supramolecular chain along the crystallo-
graphic b axis that is characterized by short NÁ Á ÁCl distances
(3.095(2) Å) and linear CÀClÁ Á ÁN angles (180°). The NÁ Á ÁCl distance
in 1 is much shorter than the sum of the effective van der Waals
radii [36,43] (ca. 3.40 Å). The adjacent one-dimensional chains
A comparison of the crystal structures of 1 and 2 showed that
there are one-dimensional supramolecular chains formed by NÁ Á ÁCl
halogen bonding and all the molecules in the same chain connect
with one other in a head-to-tail mode in both the crystal structures
of 1 and 2. This phenomenon indicates that the Cl atoms are bonded
to the opposing N atoms of the adjacent molecules selectively.
These are site-selective supramolecular syntheses, since only the
opposing N atoms are involved in the recognition processes.
connect with each other through lone pairÁ Á Á
p interaction [44]
between electron-sufficient carbonyl O atoms and the electron-
deficient triazine rings, giving rise to a two-dimensional supramo-
Table 2
Characteristic contact distances (in Å) for lone pairÁ Á Á
p interactions observed in the
crystal structure of 1a.
N1Á Á ÁO2b
3.236(2)
3.181(2)
3.319(2)
2.940(2)
C1Á Á ÁO2b
C2Á Á ÁO2b
C2cÁ Á ÁO2b
3.132(2)
3.267(2)
3.209(2)
N1cÁ Á ÁO2b
N2Á Á ÁO2b
CentroidÁ Á ÁO2b
a
b
c
The values in the table are measured in the diamond program.
Fig. 1. An ORTEP diagram of the molecular structure of 1 showing the atom-
numbering scheme and probability displacement ellipsoids drawn at the 50% level.
Symmetry code: (A) Àx, y, Àz + 1/2.
Àx, Ày + 1,Àz + 1.
Àx, y, Àz + 1/2.
Fig. 2. Supramolecular interactions in the crystal structure of 1 showing the intermolecular NÁ Á ÁCl halogen bonding (in dashed lines) and lone pairÁ Á Á
p
interactions between O
atoms on carbonyl groups and triazine rings (in dashed lines). H atoms have been removed for clarity. Symmetry codes: (A) x, y À 1, z; (B) x, Ày + 1, z À 1/2; (C) Àx, Ày + 1,
Àz + 1.

Y.-M. Zhu et al. / Journal of Molecular Structure 975 (2010) 274–279
277
Fig. 3. Crystal packing of 1 showing p–p stack between benzene rings. H atoms have been removed for clarity.
Fig. 4. An ORTEP diagram of the molecular structure of 2 showing the atom-numbering scheme and probability displacement ellipsoids drawn at the 50% level. Symmetry
code: (A) x, Ày + 1/2, z.
Table 3
Hydrogen bonding data of 2a (distances in Å; angles in degree).
DÀHÁ Á ÁA
C10ÀH10CÁ Á ÁO3b
DÀH
0.980(3)
HÁÁÁA
2.507(2)
DÁÁÁA
3.343(4)
\DHA
143.0(2)
a
The values in the table are measured in the diamond program.
xÀ1/2, y, Àz + 1/2.
b
A calculation for the molecular electrostatic potentials of 1 and 2
shows that the site selectivity can be rationalized on the basis of a
lower electrostatic potential of the opposing N atoms (À18.371 eV
for
1
and À18.381 eV for 2) than the adjacent
N atoms
(À18.366 eV for 1 and À18.375 eV for 2). It means that the opposing
N atoms are stronger electron donors than the adjacent ones. Figs. 7
and 8 show the molecular electrostatic potentials at the isodensity
surface for 1 and 2, respectively. It can be inferred from Figs. 7 and 8
that electrostatic interactions (NÁ Á ÁCl halogen bonding) can be
formed selectively between the stronger electron donors (the
opposing N atoms) and the regions of positive potential on the Cl
atoms from the adjacent molecules. Shirman et al. [13] also
reported that electrostatic potentials can be used as an effective
tool for describing the capacity of molecules to interact through
the regions of positive and negative potential on their surface.
There are obvious differences between the crystal structures 1
and 2. First, there are other different intermolecular interactions
besides halogen bonding in 1 and 2, which are lone pairÁ Á Á inter-
p
Fig. 5. A view of a double chain in 2 showing intermolecular NÁ Á ÁCl halogen
bonding (in dashed lines) and intermolecular CÀHÁ Á ÁO hydrogen bonding (in
dashed lines). H atoms of the phenyl rings have been removed for clarity. Symmetry
codes: (A) x À 3/2, y, Àz + 3/2; (B) x À 1/2, y, Àz + 3/2; (C) xÀ1, y, z.
action between carbonyl O atoms and triazine rings and p–p stack
between phenyl rings (for 1), CÀHÁ Á ÁO hydrogen bonding between
methyl groups and the O atoms of the carbonyl groups (for 2).

278
Y.-M. Zhu et al. / Journal of Molecular Structure 975 (2010) 274–279
To develop a better evaluation for the capacity of NÁ Á ÁCl halogen
bonding in the direction of the assembly of the crystal structures 1
and 2, the strengths of the NÁ Á ÁCl halogen bonding in these crystal
structures were further investigated from a theoretical perspective.
The halogen bonding complexation energy of 1 and 2 in a gas-
phase environment has been calculated as the following energy
difference:
2. The
D
Ecomplex = E(x Á x) À 2E(x) (1), where x stands for 1 or
D
Ecomplex values yield À3.44 kcal/mol for 1 and À0.34 kcal/
mol for 2. The optimized intermolecular NÁ Á ÁCl distances are
3.098 and 3.270 Å for 1 and 2, respectively. The optimized intermo-
lecular NÁ Á ÁClÀC angles in 1 and 2 are 179.99° and 179.08°, respec-
tively. These calculated distances are close to the values found in
the crystal structures [45].
In the previous literature [46–50], the theoretical values of
the strength of lone pairÁ Á Á
p
interaction are no less than
stack
À5.45 kcal/mol, the theoretical values of the strength of
p–p
Fig. 6. Crystal packing of 2 viewed along the a axis that shows one-dimensional
channels. Disordered THF solvent molecules in the channels and H atoms of the
phenyl rings have been removed for clarity.
between parallel displaced phenyl rings are À0.8 ꢀ À10.46 kcal/
mol, and the experimental and theoretical values of the interaction
energy of CÀHÁ Á ÁO hydrogen bonding are À0.77 ꢀ À2.72 kcal/mol.
Consequently, the strengths of the NÁ Á ÁCl halogen bonding in the
crystal structures 1 and 2 are comparable to those of lone pairÁ Á Á
p
interaction,
p
–p
stack and CÀHÁ Á ÁO hydrogen bonding.
4. Conclusions
A study on crystal structures and DFT calculations shows that
although the strengths of the NÁ Á ÁCl halogen bonding in the crystal
structures 1 and 2 are comparable to those of lone pairÁ Á Á
p interac-
tion,
bonding has primary directionality in the construction of these
crystal structures, leaving lone pairÁÁÁ interaction, stack and
p
–p
stack and CÀHÁ Á ÁO hydrogen bonding, the NÁ Á ÁCl halogen
p
p–p
CÀHÁ Á ÁO hydrogen bonding as auxiliary forces. An analysis of the
molecular electrostatic potentials of 1 and 2 reveals that the site
selectivity of the NÁ Á ÁCl halogen bonding results from the lower
electrostatic potential of the opposing N atoms than those of the
adjacent ones. We may use halogen bonding and molecular elec-
trostatic potential calculations to design, construct, and predict
the structures of some supramolecules to some extent.
Fig. 7. The molecular electrostatic potential at the isodensity surface of 1. Red
indicates a value greater than or equal to the maximum in negative potential and
blue indicates a value greater than or equal to the maximum in positive potential.
(For interpretation of the references to colour in this figure legend, the reader is
referred to the web version of this article.)
Acknowledgments
The authors acknowledge the financial support of National Nat-
ural Science Foundation of China (20973203) and Guangdong Nat-
ural Science Foundation (7003708).
Appendix A. Supplementary material
Crystallographic data for the structural analysis have been
deposited with the Cambridge Crystallographic Data Centre, CCDC
numbers 733851 and 733852. These data can be obtained free of
charge via http://www.ccdc.cam.ac.uk/conts/retrieving.html (or
from the Cambridge Crystallographic Data Centre, 12, Union Road,
Cambridge CB2 1EZ, UK; fax:+44 1223 336033). Supplementary
data associated with this article can be found, in the online version,
at doi:10.1016/j.molstruc.2010.04.035.
Fig. 8. The molecular electrostatic potential at the isodensity surface of 2. Red
indicates a value greater than or equal to the maximum in negative potential and
blue indicates a value greater than or equal to the maximum in positive potential.
(For interpretation of the references to colour in this figure legend, the reader is
referred to the web version of this article.)
Second, the modes of packing of the chains formed by halogen
bonding in the crystal structures 1 and 2 are also different. Based
on the above results, it can be concluded that the NÁ Á ÁCl halogen
bonding take the priority to direct the assembly of the crystal
structures 1 and 2, as there are the similar one-dimensional chains
formed by NÁ Á ÁCl halogen bonding in both the case of 1 and 2 and
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