Structures of N,N′,N′′-tris(3-pyridinyl)-1,3,5-benzenetricarboxamide and its nano-scopic zinc(II) coordination ring and their interaction with calf thymus DNA

Article abstract of DOI:10.1016/j.molstruc.2008.10.028

N,N′,N′′-tris(3-pyridinyl)-1,3,5-benzenetricarboxamide monohydrate 3-TPB·H₂O and an unprecedented cyclic dimeric oligoamide zinc complex [Zn₂(3-TPB)₂Cl₄]·2H₂O (1) have been synthesized and their cryst

Full text of DOI:10.1016/j.molstruc.2008.10.028

Journal of Molecular Structure 920 (2009) 18–22
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Journal of Molecular Structure
journal homepage: www.elsevier.com/locate/molstruc
Structures of N,N0,N00-tris(3-pyridinyl)-1,3,5-benzenetricarboxamide and its
nano-scopic zinc(II) coordination ring and their interaction with calf thymus DNA
a
Tiantian Jia a, Yongmei Zhao a, Feifei Xing a, Min Shao b, Shourong Zhu a, , Mingxing Li
*
a Department of Chemistry, College of Sciences, Shanghai University, #99 Shangda Road, Shanghai 200444, China
b Instrumental Analysis and Research Center, Shanghai University, Shanghai 200444, China
a r t i c l e i n f o
a b s t r a c t
N,N0,N00-tris(3-pyridinyl)-1,3,5-benzenetricarboxamide monohydrate 3-TPBꢀH2O and an unprecedented
cyclic dimeric oligoamide zinc complex [Zn2(3-TPB)2Cl4]ꢀ2H2O (1) have been synthesized and their crys-
tal structure were reported. Different from anhydrous 3-TPB, which is s-conformation, 3-TPBꢀH2O adopts
aas-conformation. All amide hydrogen form H-bonds. Zn ion in dimeric [Zn2(3-TPB)2Cl4]ꢀ2H2O located in
a tetrahedron coordination environment. Two 3-TPB ligands and two Zn(II) ions link alternatively to form
a 28-membered ring. The Znꢀ ꢀ ꢀZn distance in the ring is 11.162(5) Å. One pyridine nitrogen atom is free.
The nano-size macrocyclic framework of 1 is stable up to 390 °C. 3-TPBꢀH2O and complex 1 have similar
fluorescence emission ꢁ450 nm. Fluorescence titration shows that calf thymus DNA can quench the fluo-
rescence 3-TPB in aqueous solution. However, calf thymus DNA has no interaction with complex 1.
Ó 2008 Elsevier B.V. All rights reserved.
Article history:
Received 26 August 2008
Received in revised form 8 October 2008
Accepted 12 October 2008
Available online 31 October 2008
Keywords:
Oligoamide
Zinc complexes
Calf thymus DNA
X-ray crystallography
1. Introduction
ANH moiety acts as a hydrogen donor and the AC@O group acts
as a hydrogen acceptor. Palmans constructed hydrogen-bonded
Organic Amides have been paid much attention not only for
their relating to peptide, but also for the advantages on the assem-
bly of supramolecular networks organized by hydrogen bond. [1–
4]. Several pyridine-derived foldamers have been utilized to mimic
the binding surfaces of protein helices [2]. In recent years signifi-
cant progress has been made in the design of synthetic oligoamide
nano-tube, representing potentially a new and important class of
functional materials [5–8]. However, Study based on metal-con-
taining cyclic amides is still rare. Puddephatt and coworkers re-
ported a construction of a metal-containing molecular triangle
taking advantage of dipyridylamides (N-pyridin-4-ylisonicotina-
mide) as a bridging ligand. The complex cation forms a dimeric/tri-
meric architecture by 2 + 2 or 3 + 3 self-assembly of rigid or
flexible oligoamide with palladium(II), which is similar to that
formed by cyclic peptides [9,10]. On the other hand, the design
of synthetic compounds that can read the information in the nu-
cleic acid in particular DNA duplex has been a central goal at the
interface of chemistry and biology [11]. The interactions of some
oligoamides and DNA have been exploited [11–13]. It was found
that oligoamide compounds bind to DNA in the minor groove
[12,13].
porous solid derived from 3-TPB [14]. Stang and coworkers have
utilized 3-TPB to construct a Pd(II) coordination cage with the
(Pd3L2)6+ moiety [15]. Lah and coworkers reported [Pd6(3-
TPB)8]12+ cages two years later [16]. [Cu6(3-TPB)8]12+ nano-cages
can be formed in DMSO [17]. Mononuclear Cu(I), Ag(I) complexes
of the N-methyl substituted 3-TPB have also been reported. All pyr-
idine nitrogen atoms coordinated to metal ion [18]. In the reported
complexes, all three pyridine nitrogen atoms were utilized to form
monomer, cage, or polymer complex. There is no dimeric complex
reported yet. We are also interested in pyridine-containing amide
ligands and their complexes [19,20]. We report herein the solid-
state structures of 3-TPB and its dimeric nano-size macrocyclic
complex assembled from 3-TPB and ZnCl2, luminescence proper-
ties of these two compounds and their interaction with calf thymus
DNA.
2. Experimental
2.1. General information
All chemicals were of reagent grade and used as received with-
out further purification. Calf thymus DNA (CT-DNA) was purchased
from Sigma and was sonicated and purified as described preciously
[21]. Elemental analyses were performed on a Vario EL III elemen-
tal analyzer. Infrared spectra were recorded with a Nicolet A370
N,N0,N00-tris(3-pyridinyl)-1,3,5-benzenetricarboxamide (3-TPB)
is a fascinating functional group that can serve as active base sites
and which possesses two types of hydrogen bonding sites: the
FT-IR spectrometer by KBr pellets in the range 400–4000 cmꢂ1
.
* Corresponding author.
E-mail address: shourongzhu@shu.edu.cn (S. Zhu).
Thermogravimetric analyses were completed on a Netzsch STA
0022-2860/$ - see front matter Ó 2008 Elsevier B.V. All rights reserved.
doi:10.1016/j.molstruc.2008.10.028

T. Jia et al. / Journal of Molecular Structure 920 (2009) 18–22
19
449C thermal analyzer at a heating rate of 10 °C minꢂ1 in air. Fluo-
Table 1
Crystallographic data for 3-TPBꢀH2O and 1.
rescent spectra were recorded on
a
Shimadzu RF-5301
spectrophotometer.
Compounds
3-TPBꢀH2O
1
Formula
C24H20N6O4
456.46
273(2)
Monoclinic
Cc
17.757(2)
14.549(2)
8.3497(10)
90
99.961(2)
90
2124.6(5)
4
1.427
0.101
C24H20Cl2 N6O4Zn
592.73
296(2)
monoclinic
P2(1)/n
13.871(8)
14.633(9)
13.871(8)
90
118.41
90
2476(3)
4
1.590
2.2. Synthesis of 3-TPBꢀH2O
Formula weight
Temp. (K)
Crystal system
Space group
a (Å)
3-TPB was prepared in a one-step reaction between 3-amino-
pyridine and 1,3,5-benzene tricarboxylate chloride in dry THF in
the presence of triethylamine following a reported procedure
[14,22]. 3-TPB (0.438 g) was dissolved in 5 mL DMF. After filtration,
the solution was allowed to stand at room temperature for a week,
Light yellow crystals suitable for X-ray crystal analysis settled
gradually in 35% Yield.
b (Å)
c (Å)
a
(°)
b (°)
c
(°)
V (Å3)
Z
Dc (mg mꢂ3
)
2.3. Synthesis of [Zn2(3-TPB)2Cl4]ꢀ2H2O
Abs coeff. (mmꢂ1
)
1.252
F(000)
952
5358
1878
211
1208
12693
4380
342
[Zn2(3-TPB)2Cl4]ꢀ2H2O was readily achieved by reaction of 3-
TPB with ZnCl2 in the molar ratio of 1:1 solvothermally at 110 °C
Reflns collections
Unique reflns
Params
in ethanol.
A mixture of ZnCl2 (6.8 mg, 0.050 mmol), 3-TPB
GOF on F2
0.892
1.013
(21.9 mg, 0.050 mmol) and EtOH 10 ml was heated at 110 °C for
3 d. Light yellow crystals were obtained when the mixture was
cooled to room temp at 10 °C hꢂ1, (74.4% yield based on 3-TPB).
FTIR (KBr, cmꢂ1): 1686 (s), 1663 (m), 1584 (m), 1542 (vs), 1484
(m), 1419 (s), 1331(m), 1281 (m). Anal. Calcd for {[Zn(3-TPB)
Cl2]ꢀH2O} C24H20Cl2N6O4Zn:C, 48.63; H, 3.40; N, 14.18. Found: C,
48.40; H, 3.54; N, 14.07.
R1, wR [I > 2
r
(I)]
0.0679, 0.1941
0.0694, 0.1981
0.414 and ꢂ0.536
0.0466, 0.0951
0.0834, 0.1110
0.372 and ꢂ0.410
R1, wR (all data)
Largest diff. peak and hole (e Åꢂ3
)
Table 2
Selected bond length (Å) and angle (°) of complex 1.
Zn(1)AN(4)#1
Zn(1)ACl(2)
N(4)#1AZn(1)ACl(2)
N(1)AZn(1)ACl(2)
N(4)#1AZn(1)AN(1)
2.036(3)
Zn(1)AN(1)
Zn(1)ACl(1)
N(4)#1AZn(1)ACl(1)
N(1)AZn(1)ACl(1)
Cl(2)AZn(1)ACl(1)
2.041(3)
2.4. Fluorescence titration experiments
2.2032(17)
106.36(9)
104.98(9)
112.78(13)
2.2358(14)
101.64(10)
110.85(10)
120.35(6)
The concentration of DNA was determined by visible absor-
bance measurement using extinction coefficient e260
=
12824 Mꢂ1 cmꢂ1. The purity of the DNA samples were confirmed
by a spectrophotometer, A260/A280 ranges between 1.8 and 2.0.
The 2.4 mM CT-DNA stock solution was always resuspended in
BPE (bis-phosphate EDTA) buffer (6.0 mM Na2HPO4, 2.0 mM NaH2-
PO4, 1.0 mM EDTA, pH = 7.0) for the measurement. The 3-TPB and 1
were first dissolved in dimethylsulfoxide (DMSO) at 0.23 M (for 3-
TPB) or 0.17 M (for 1) and then further diluted with water. Stock
solutions were kept at 4 °C and freshly diluted to the desired con-
centration prior to use. Titration experiments were carried out in
aqueous solution unless noted otherwise. Fluorescence emission
(excited at 287 nm) was monitored over the range 350–550 nm.
from methanol, which was reported previously [14], the light yel-
low, rectangle-shaped 3-TPBꢀH2O crystals were formed in DMF.
According to the relative position of the amide oxygen and pyridyl
nitrogen atom to amide nitrogen, 3-TPB adopts different conforma-
tions in crystal structures as illustrated in Chart 1. s-Conformation
indicates the pyridine nitrogen atom and the amide oxygen atom
are in the same side of amide nitrogen, while a-conformation indi-
cates the two atoms are trans each other (Chart 1). The crystal
structures demonstrate that anhydrous 3-TPB [14] is a highly sym-
metric molecule (a-conformation) while hydrated 3-TPBꢀH2O is in
aas-conformation. All three pyridine amide groups in 3-TPB are
identical, thus all three pyridine amide are in trans position (a-con-
formation). In hydrated 3-TPBꢀH2O however, the symmetry is
much lower and the three pyridine amide are different. The three
pyridine amides in 3-TPBꢀH2O are cis, cis, trans, respectively, (ssa-
conformation). The dihedral angles between amide CNO and ben-
zene is in the ranges from 32.02(37)° to 34.74(38)°. While the dihe-
dral angle between amide CNO and pyridine ranges from 26.4(5)°
(N(4)-containing pyridine) to 60.63(37)° (N(6)-containing pyri-
dine). 3-TPBꢀH2O packed into a monolayer and the monolayer
packed into 3D structure (Fig. S1). There are not much difference
in bond distances and bond angles between 3-TPBꢀH2O and 3-
TPB, but the arrangement of the pyridine amide and dihedral an-
gles are fundamental different. Additionally, different from the bi-
layer supramolecular structure assembled by anhydrous 3-TPB
[14], the monolayer structure is formed (Fig. S1) by hydrated 3-
TPB due to the different dihedral angles defined by pyridine ring
and center benzene ring in anhydrous 3-TPB and hydrated 3-TPB.
Water molecule and all amide hydrogen atoms form H-bonds as
expected. H-Bond distances and angles are listed in Table 3. H-
bond links adjacent N,N0,N00-tris(3-pyridinyl)-1,3,5-benzenetricarb-
oxamide in 3-TPBꢀH2O (Fig. S2).
3-TPB (38
centration varies from 0.9
l
M) aqueous solutions were used for titration. DNA con-
M to 0.03 mM bp. In this case, volume
l
change is less than 5% in the whole titration process.
2.5. X-ray crystallography
Single crystal diffraction data were collected on a Bruker Smart
Apex-II CCD diffractometer with graphite monochromatic Mo K
a
radiation (k = 0.71073 Å) at room temperature. Empirical absorp-
tion corrections were applied using SADABS program [23]. The
structures were solved by direct method with SHELXS-97 program
and refined by full-matrix least squares on F2 with SHELXL-97 pro-
gram [24,25]. All none-hydrogen atoms were refined anisotropi-
cally and hydrogen atoms were placed geometrically if possible.
The crystal data and refinement results are given in Table 1. The se-
lected bond distances and angles are presented in Table 2. H-bonds
are listed in Table 3.
3. Results and discussion
3.1. Description of crystal structures
Fig. 1 shows the structures of 3-TPBꢀH2O. In contrast to the
transparent, hexagon-shaped crystals of anhydrous 3-TPB obtained

20
T. Jia et al. / Journal of Molecular Structure 920 (2009) 18–22
Table 3
In [Zn2(3-TPB)2Cl4]ꢀ2H2O (1), each Zn(II) ion is four-coordinated
by two nitrogen atoms from different 3-TPB and two chloride an-
ions to form a tetrahedron environment (Fig. 2). Two 3-TPB ligands
and two Zn(II) ions link alternatively to form a 28-membered ring.
The Znꢀ ꢀ ꢀZn distance in the ring is 11.162(5) Å, which is shorter
Hydrogen bonds for 3-TPBꢀH2O and complex 1 (Å) and angle (°).
DAH. . .A
d(DAH)
d(H. . .A)
d(D. . .A)
<(DHA)
3-TPBꢀH2O
N(2)AH(2N)AO(1W)
N(3)AH(3N)AO(2)
N(5)AH(5N)AO(3)
O(1W)AH(1AW)AN(4)
O(1W)AH(1BW)AN(6)
0.84(4)
0.87(3)
0.96(3)
0.97
1.94(5)
1.95(3)
2.13(3)
1.87
2.767(4)
2.785(3)
3.056(3)
2.836(4)
2.866(4)
166(4)
161(3)
163(3)
173.3
compared with the Cuꢀ ꢀ ꢀCu distances in
a nano-cage of
13.940(3) Å [17]. This distance is much longer than a flexible oli-
goamide Zn complex of 3.572 Å [26]. In complex 1, ligand 3-TPB
adopts ass-conformation. The two coordinated pyridine amides
are in a- and s-conformation, respectively, and the uncoordinated
pyridine amide adopts s-conformation, which is quite different
from the a- or s-conformation of the Cu(II) complex of 3-TPB and
its Ag(I) and Pd(II) complex in a-conformation. ZnAN distance of
2.04 Å is comparable with that in Cu(II) complex of 2.03 Å [18],
while ZnACl bond lengths are in the ranges from 2.20 to 2.24 Å.
Similar to other complexes based on amide/peptide ligands,
hydrogen bonds interactions play very important role in crystal
packing of complex 1(Figs. S3 and S4). The uncoordinated pyridine
nitrogen atom (N6) and the amide nitrogen atom (N5) outside the
nano-ring both form hydrogen bonds with O4 atom from lattice
water molecule with the distances of 2.804 and 2.734 Å, respec-
tively, (Table 3). In addition, the amide nitrogen atom (N2) in the
nano-ring also forms hydrogen bond with Cl1 anion and the
Cl1. . .N2 distance is 3.253(4) Å. The distance of Cl1 and N3 is much
longer with 3.405(4) Å (Table 3). The adjacent cyclic oligoamide
complex molecules are packed to form bi-layered structure from
a-axis (Fig. S3). Cl1. . .N2, N6. . .O4 H-bonds further assemble the
bilayers into 3D supramolecular structure as shown in Fig. S4. All
the H-bonds link adjacent bilayers. Intramolecular H-bonds does
not exist in complex 1. This phenomenon is quite different from
that in dimeric complex of flexibly oligoamide [10]. The dihedral
angle defined by pyridine ring and center benzene ring in hydrated
3-TPBꢀH2O and 1 are different, 3-TPBꢀH2O looks flatter than that of
1 (Fig. S5).
0.89
2.00
162.2
Symmetry transformations used to generate equivalent atoms: #1x, ꢂy + 2, z ꢂ 1/2
#2x, ꢂ y + 2, z + 1/2.
1
O(4)AH(4B). . .N(6)#2
N(5)AH(5A). . .O(4)#3
N(3)AH(3A). . .Cl(1)#4
N(2)AH(2A). . .Cl(1)#5
0.852(10)
0.86
0.86
1.90(3)
1.99
2.60
2.734(6)
2.801(6)
3.405(4)
3.253(4)
166(10)
157.4
157.5
0.86
2.47
152.0
Symmetry transformations used to generate equivalent atoms: #1 ꢂx, ꢂy, ꢂz #2x, y,
z ꢂ 1 #3x ꢂ 1/2, ꢂy + 1/2, z + 1/2, #4x + 1, y, z + 1 #5x + 1/2, ꢂy + 1/2, z + 1/2.
The thermal stability of complex 1 was examined by thermo-
gravimetric analysis (TGA). The TGA curve (Fig. S6) shows that
the first plateau (to 160 °C) lost 3.10% corresponding to the loss
of one water molecule (calcd 3.03%). The framework remains un-
changed up to 375 °C. The thermal stability of complex 1 is obvi-
ously higher than [Cd(3-TPB)2Cl2]n reported by Tzeng et al. [27].
Fig. 1. ORTEP drawing of 3-TPBꢀH2O with hydrogen atoms omitted for clarity (30%
thermal ellipsoids probability).
#
N
3.2. Solid-state emission spectra
#
*
N
N
*
#
NH
O
NH
O
The emission spectra of 3-TPB and complex 1 are investigated in
solid-state at room temperature (Fig. 3). As expected, 3-TPB and its
Zn(II) complex are both luminescent in the solid-state. Upon exci-
tation at 389 nm, 3-TPB shows a broad emission with a maximum
at ca. 450 nm, which is almost identical to excited at 300 nm [27].
Complex 1 displays a similar emission, but splits into two peaks at
450 and 471 nm, which is also quite similar to the 2D coordination
polymer [Ag(3-TPB)PF6]n [27]. When excited at 287 nm, the emis-
sions are essentially the same (Fig. 2, inset). Due to the close sim-
ilarity of emissions between the ligand and its complex, these
emissions can be ascribed to an intraligand transition [27].
N
#
O
N
H
O
N
H
*
*
HN
O
HN
O
*
*
N
#
# N
s-TPB
a-TPB
#
#
N
#
N
N
*
*
O
*
*
O
O
O
N
#
3.3. DNA-binding affinity
N
H
N
H
N
H
N
H
The DNA-binding affinity was measured in aqueous solution
using the intrinsic fluorescence of 3-TPB (Fig. 4). Fluorescence
emission spectra were recorded with excitation at 287 nm and
emission at 425 nm. Fig. 4 shows the fluorescence spectra (ex
287 nm) of 3-TPB in the absence and presence of CT-DNA. The
presence of CT-DNA can quench the fluorescence emission of 3-
TPB in aqueous solution. The steady-state fluorescence of free 3-
TPB is quenched by double strand nucleic acid. Binding isotherms
were obtained by measuring fluorescence of a fixed concentration
HN
O
HN
O
*
*
#
#
N
N
ssa-TPB
aas-TPB
Chart 1. Conformations observed for 3-TPB in crystal structures.

T. Jia et al. / Journal of Molecular Structure 920 (2009) 18–22
21
Fig. 2. ORTEP drawing of complex 1 with hydrogen atoms omitted for clarity (30% thermal ellipsoids probability).
also examine the interaction of complex 1 with calf thymus DNA
at the same condition, the result demonstrate that there no signif-
icant interaction, possibly due to bulky of the complex.
150
100
50
450
300
150
3-TPB
1
1
4. Conclusions
3-TPB
0
350
400
450
500
550
In summary, 3-TPBꢀH2O and a nano-size cyclic oligoamide Zn(II)
complex [Zn2(3-TPB)2Cl4]ꢀ2H2O was synthesized. H-bond play
important role in crystal packing. The framework of the [Zn2(3-
TPB)2Cl4] can be stable up to 375 °C. Both 3-TPB and [Zn2(3-
TPB)2Cl4]ꢀ2H2O exhibit intraligand emission peaks at ꢁ460 nm
upon excitation at 389 or 287 nm. Free 3-TPB can interact with
CT-DNA in aqueous solution, but complex 1 cannot.
wavelength(nm)
Acknowledgment
400
450
500
550
600
wavelength(nm)
This work was supported by the Start-up Foundation of Shang-
hai University and Development Foundation of Shanghai Municipal
Education Committee, China (Grant No. 215 06AZ098).
Fig. 3. Solid-state emission spectra of 3-TPB and complex 1 measured at room
temperature with an excitation wavelength at 389 nm and 287 nm (inset).
Appendix A. Supplementary data
Increase DNA concentration
440
Crystallographic data for the structural analyses have been
deposited with the Cambridge Crystallographic Data Center, CCDC
Ref. Nos. 694563 (for monohydrate ligand) and 694564 (complex
1). Copies of the data can be obtained free of charge from CCDC,
12 Union Road, Cambridge, CB2IEZ, UK. E-mail: deposit@ccdc.ca-
m.ac.uk. Supplementary data associated with this article can be
found, in the online version, at doi:10.1016/j.molstruc.2008.
10.028.
400
400
360
300
320
-6.0
-5.5
log([DNA],M)
-5.0
-4.5
200
100
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