Binding of polyatomic anions with protonated ureido-pyridyl ligands

Article abstract of DOI:10.1021/cg101595n

Two ureido-pyridyl ligands, 1-(4-nitro-phenyl)-3-pyridine-3-ylmethyl-urea (L¹) and 1-pentafluorophenyl-3-pyridine-4-yl-urea (L²) were synthesized in good yields, and solid-state anion binding studies of (HL¹)⁺ and (HL²)⁺ with polyatomic anions such as NO₃^-, AcO^-, ClO₄ ^-, SO₄^2-, and SiF₆^2- were carried out in detail. Protonation of the pyridyl nitrogen center of L ¹ with HNO₃, HClO₄, and HF in different solvent media yielded crystals of complexes 1 (HL¹ · NO₃), 2 (HL¹ · ClO₄), and 3 (HL¹ · 0.5SiF₆) suitable for single crystal X-ray diffraction studies, respectively. Similarly, protonation of L² with HNO₃, CH₃COOH, and H₂SO₄ yielded single crystals of complexes 4 [2(HL² · NO₃) ·DMF], 5 (HL ² · AcO), and 6 [(HL²)₂ · SO ₄], respectively. X-ray crystallographic analysis of all these six complexes has been carried out and the details of anion binding with the urea functionality of ureido-pyridyl ligands were investigated. In all the complexes, the pyridyl moiety of the ligands is found to be protonated and the binding of anions are observed at the urea functionality of the ligands through the R ₂²(8) hydrogen bonding motif irrespective of sizes and shapes of anions or the electron withdrawing ability of aryl substitutions (p-nitro phenyl vs pentafluoro phenyl) or the position of the pyridyl nitrogen center (protonation site) of the designed ligands.

Full text of DOI:10.1021/cg101595n

ARTICLE
pubs.acs.org/crystal
Binding of Polyatomic Anions with Protonated Ureido-pyridyl Ligands
Published as part of a virtual special issue on Structural Chemistry in India: Emerging Themes
S. Marivel, M. Arunachalam, and Pradyut Ghosh*
Department of Inorganic Chemistry, Indian Association for the Cultivation of Science, 2A & 2B Raja S. C. Mullick Road, Kolkata 700 032, India
ABSTRACT: Two ureido-pyridyl ligands, 1-(4-nitro-phenyl)-3-pyridine-3-ylmethyl-urea (L1) and
1-pentafluorophenyl-3-pyridine-4-yl-urea (L2) were synthesized in good yields, and solid-state
anion binding studies of (HL1)þ and (HL2)þ with polyatomic anions such as NO3-, AcO-,
ClO4-, SO42-, and SiF62- were carried out in detail. Protonation of the pyridyl nitrogen center of
L1 with HNO3, HClO4, and HF in different solvent media yielded crystals of complexes 1
(HL1 NO3), 2 (HL1 ClO4), and 3 (HL1 0.5SiF6) suitable for single crystal X-ray diffraction
3
3
3
studies, respectively. Similarly, protonation of L2 with HNO3, CH3COOH, and H2SO4 yielded
single crystals of complexes 4 [2(HL2 NO3) DMF], 5 (HL2 AcO), and 6 [(HL2)2 SO4],
respectively. X-ray crystallographic analysis of all these six complexes has been carried out and the
details of anion binding with the urea functionality of ureido-pyridyl ligands were investigated. In all
the complexes, the pyridyl moiety of the ligands is found to be protonated and the binding of anions
3
3
3
3
2
are observed at the urea functionality of the ligands through the R2 (8) hydrogen bonding motif
irrespective of sizes and shapes of anions or the electron withdrawing ability of aryl substitutions (p-nitro phenyl vs pentafluoro phenyl) or
the position of the pyridyl nitrogen center (protonation site) of the designed ligands.
’ INTRODUCTION
In these cases, the metal-center plays the role in determining
the orientation of the receptor units thus by changing the
hydrogen bonding patterns. Study of anion binding and anion
assisted formation of supramolecular architecture by protonated
ureido-pyridyl ligands could be useful in the area of anion
coordination chemistry.9d-h Thus, the interference of the catio-
nic counterpart, such as metal ions or tetraalkylammonium ions,
can be avoided in the anion binding event. An interesting contribu-
tion by Gale et al. has shown the importance of cobinding of proton
and chloride toward transport of HCl with some amidopyrrole-
based ligands in biological systems.10 Herein we report two new
ureido-pyridyl ligands, 1-(4-nitro-phenyl)-3-pyridine-3-ylmethyl-
urea and 1-pentafluorophenyl-3-pyridine-4-yl-urea, and structu-
Anion binding/recognition in synthetic receptors as well as in
biological systems is one of the most frontier and emergent areas
of research in supramolecular chemistry and it plays many
significant roles in different areas of chemistry and biology.1
Anions have shown enormous potential applications in medicine,
catalysis, environment, ion exchange, anion separation in nuclear
waste, water purification, etc.1 In general, organic compounds
that are capable of forming hydrogen bonds (e.g., those contain-
ing -NH fragments) have been widely studied for coordination of
different anions. To date a number of anion recognition elements
such as protonated amine,2 amide,3 urea,4 pyrrole,5 indole,6 and
guanidinium7 have been developed. In particular, urea-based
ligands, good hydrogen bond donors to anions, have attracted
lots of interest toward the development of selective anion
receptors as well as anion sensors.4 Two -NH of urea can
participate in the binding of anions with various H-bond motifs
due to their unidirectional hydrogen bonding nature. It is evident
from the crystal structures of many urea based ligands that the
most prominent hydrogen bonding pattern is the robust R-
rally demonstrate anion binding properties of these ligands in
-
their protonated form with polyatomic anions such as NO3
,
AcO-, ClO4-, SO42-, and SiF62-. In all the complexes, ligands
L1 and L2 were found to be protonated and the primary binding
2
of anion always occurs at the urea moiety, through the R2 (8)
recognition patterns of strong N-H O hydrogen bonds, even
3 3 3
though the two-dimensional arrangement of the resulting pro-
duct changing depending upon the substitution on the phenyl
ring of ligand and the counteranion.
network, a tape of bifurcated N-H O hydrogen bonds
3 3 3
between N-H donors and an oxygen acceptor.8 On the other
hand, the urea moiety has immense potential to interact with a
variety of anions through the formation of different hydrogen
’ EXPERIMENTAL SECTION
2
2
bonding patterns R1 (6) for halides, R2 (8) for planar, tetrahe-
dral, or octahedral anions (Scheme 1). Several ureido-pyridyl
ligands have been utilized as synthons in crystal engineering as
well as receptors for anion binding by different groups.9 For
example, Steed et al. have reported a range of anion binding
coordination complexes of ureido-pyridyl ligands where the ligand
complexes with a metal cation and its conjugate anion.9a-c
Materials and Methods. 3-Picolylamine and 4-aminopyridine
were purchased from Fluka and used as received. 4-Nitrophenyl
Received: November 30, 2010
Revised:
February 8, 2011
Published: March 11, 2011
r
2011 American Chemical Society
1642
dx.doi.org/10.1021/cg101595n Cryst. Growth Des. 2011, 11, 1642–1650
|

Crystal Growth & Design
ARTICLE
2
1
Scheme 1. (a) The R2 (8) and (b) R2 (6) Hydrogen Bonded
Motifs Observed in the Urea Based Ligands with Oxy-Anions
and Metal-Bound Halogens, Respectively
146.81, 154.71. Elemental analysis calcd: C, 46.57; H, 3.91; N, 20.89.
Found: C, 46.23; H, 3.83; N, 20.92.
Synthesis of Complex HL1 ClO4, 2. Complex 2 was obtained by
3
adding 0.2 mL of 70% perchloric acid to 10 mL acetone solution of L1
(272.26 mg, 1 mmol). After the addition of acid, the clear solution was
filtered and kept for crystallization at room temperature. Pale-yellow
crystals suitable for X-ray crystallography were obtained after 2-3 days.
Yield of 2: 71%; 1H NMR (DMSO-d6, 300 MHz) δ (ppm) 4.52 (d, 2H),
7.15 (t, 1H, -NH), 7.62 (d, 2H), 8.06 (t, 1H), 8.13 (d, 2H), 8.54 (1H),
8.82 (1H), 8.86 (s, 1H), 9.64 (s, -NH). 13C NMR (75 MHz, DMSO-d6)
δ (ppm) 40.85, 117.80, 125.69, 127.48, 140.83, 141.03, 141.28, 145.41,
147.35, 155.30. Elemental analysis calcd: C, 41.89; H, 3.52; N, 15.03.
Found: C, 41.26; H, 3.23; N, 15.28.
Synthesis of Complex HL1 0.5SiF6, 3. Complex 3 was obtained by
3
adding 0.1 mL of 48% hydrofluoric acid to the acetone solution of L1
(272.26 mg, 1 mmol). After the addition of acid, the clear solution was
filtered and kept for crystallization at room temperature. Pale-yellow
crystals suitable for X-ray crystallography were obtained after 4-5 days.
Yield of 3: 38%. 1H NMR (DMSO-d6, 300 MHz) δ (ppm) 4.51 (d, 2H),
7.15 (t, 1H, -NH), 7.65 (d, 2H), 8.04 (t, 1H), 8.14 (d, 2H), 8.50 (1H),
8.80 (1H), 8.84 (s, 1H), 9.63 (s, -NH). 13C NMR (75 MHz, DMSO-d6)
δ (ppm) 40.84, 117.73, 125.66, 127.32, 140.59, 141.30, 141.48, 144.93,
147.32, 155.29. Elemental analysis calcd: C, 45.35; H, 3.81; N, 16.27.
Found: C, 45.16; H, 3.57; N, 16.21.
isocyanate and pentafluorophenylisocyanate were purchased from Sig-
ma-Aldrich and used as received. Methanol (MeOH), chloroform
(CHCl3), tetrahydrofuran (THF), acetone, dimethylformamide (DMF),
and diethylether were purchased from Spectrochem-India and distilled prior
to use. 48% Hydrofluoric acid, 69% nitric acid, 70% perchloric acid, glacial
acetic acid, and sulphuric acid were purchased from Merck, India, and used
as received without any further purification.
Physical Measurements. H and 13C NMR spectra were re-
1
corded on Bruker 300 and 75 MHz or Bruker 500 and 125 MHz FT-
NMR spectrometers, respectively, and the chemical shifts are reported in
parts per million. Elemental analyses for the synthesized ligands and
complexes were carried out with a 2500 series II elemental analyzer
(Perkin-Elmer, Waltham, MA).
Synthesis of Complex 2(HL2 NO3) DMF, 4. Complex 4 was obtained
3
3
by adding 0.2 mL of 69% nitric acid to 10 mL dimethylformamide
solution of L2 (303.19 mg, 1 mmol). After the addition of acid, the clear
solution was filtered and kept for crystallization at room temperature.
Colorless crystals suitable for X-ray crystallography were obtained after
4-5 days. Yield of 4: 68%; 1H NMR (DMSO-d6, 500 MHz) δ (ppm)
7.43 (d, 2H, Ar-CH), 8.35 (d, 2H, Ar-CH), 8.79 (b, 1H, -NH), 9.61 (b,
1H, -NH). 13C NMR (125 MHz, DMSO): δ 112.49, 146.22, 150.09,
151.79. Elemental analysis calcd: C, 40.26; H, 2.63; N, 15.65. Found: C,
40.02; H, 2.12; N, 15.52.
Syntheses. Synthesis of L1. 3-Picolylamine (0.61 mL, 6 mmol) was
dissolved in 50 mL of CHCl3 and the mixture was stirred at RT for 10 min
under nitrogen atmosphere. Then 4-nitrophenylisocyanate (0.985 g, 6 mmol)
was added to the above solution with constant stirring. The formation of a
yellow precipitate in the reaction mixture was observed immediately and
was allowed to stir for 10 h. The precipitate was filtered, and the residue was
washed with CHCl3 (3 ꢀ 10 mL) and with diethyl ether. The product was
dried in a vacuum to give a crystalline yellow powder of 1. Yield: 72%. 1H
NMR (300 MHz, DMSO-d6): δ 4.35 (d, 2H, -CH2), 7.02 (t, 1H, NH),
7.35 (t, 1H, Ar-CH), 7.63 (d, 2H, Ar-CH), 7.72 (d, 1H, Ar-CH), 8.13 (d,
2H, Ar-CH), 8.45 (d, 1H Ar-CH), 8.54 (s, 1H, Ar-CH), 9.43 (s, 1H, -NH).
13CNMR(75MHz, D2O): δ41.17, 117.70, 124.13, 125.74, 135.71, 135.97,
141.15, 147.63, 148.75, 149.40, 155.16. Elemental analysis calcd: C, 57.35;
H, 4.44; N, 20.58. Found: C, 57.27; H, 4.41; N, 20.52.
Synthesis of Complex HL2 AcO, 5. Complex 5 was obtained by
3
adding 0.1 mL of glacial acetic acid to the 10 mL methanolic solution of
L2 (303.19 mg, 1 mmol). After the addition of acid, the clear solution was
filtered and kept for crystallization at room temperature. Colorless
crystals suitable for X-ray crystallography were obtained after 3-4 days.
1
Yield of 5: 59%; H NMR (MeOD, 500 MHz) δ (ppm) 2.01 (s, 3H,
CH3COO-), 7.57 (d, 2H, Ar-CH), 8.38 (d, 2H, Ar-CH). 13C NMR
(125 MHz, MeOD): δ 113.07, 148.99. Elemental analysis calcd: C,
46.29; H, 2.77; N, 11.57. Found: C, 46.10; H, 2.52; N, 11.23.
Synthesis of L2. 4-Aminopyridine (940 mg, 10 mmol) was dissolved
in 50 mL of THF and the mixture was stirred for 10 min under a nitrogen
atmosphere at RT. Pentafluoro phenylisocyanate (1.3 mL, 10 mmol,
1 equiv) was added through a syringe under nitrogen atmosphere with
constant stirring. The formation of a white precipitate in the reaction
mixture was observed immediately and was allowed to stir for 10 h. The
precipitate was filtered, and the residue was washed thoroughly with
THF (3 ꢀ 10 mL). Then the residue was further washed with diethyl
ether and dried in air to give 2.6 g of white powder of 2. Yield: 86%. 1H
NMR (500 MHz, DMSO-d6): δ 7.42 (d, 2H, Ar-CH), 8.35 (d, 2H, Ar-
CH), 8.72 (b, 1H, -NH), 9.53 (b, 1H, -NH). 13C NMR (125 MHz,
DMSO): δ 112.44, 146.03, 150.17, 151.73. Elemental analysis calcd: C,
47.54; H, 1.99; N, 13.86. Found: C, 47.48; H, 1.91; N, 13.52.
Synthesis of Complex (HL2)2 SO4, 6. Complex 6 was obtained by
3
adding 0.1 mL of conc. sulphuric acid to the 10 mL methanolic solution
of L2 (303.19 mg, 1 mmol). After the addition of acid, the clear solution
was filtered and kept for crystallization at room temperature. Colorless
crystals suitable for X-ray crystallography were obtained after a week.
Yield of 5: 34%; 1H NMR (DMSO-d6, 300 MHz) δ (ppm) 7.92 (d, 2H,
Ar-CH), 8.64 (d, 2H, Ar-CH), 9.37 (s, -NH), 10.86 (s, -NH). 13C NMR
(755 MHz, DMSO-d6,): δ 114.10, 142.71, 151.89, 154.28. Elemental
analysis calcd: C, 40.92; H, 2.00; N, 11.93. Found: C, 40.76; H, 1.97;
N, 11.79.
X-ray Measurement and Structure Determination. The crystallo-
graphic data and details of data collection for complexes 1-6 are given in
Table 1. In each case, a crystal of suitable size was selected from the
mother liquor, immersed in paratone oil, then mounted on the tip of a
glass fiber, and cemented using epoxy resin. The intensity data for all six
crystals were collected using MoKR (λ = 0.7107 Å) radiation on a
Bruker SMART APEX diffractometer equipped with a CCD area
detector at 100 K. The data integration and reduction were processed
with SAINT11a software. An empirical absorption correction was applied
to the collected reflections with SADABS.11b Structures were solved by
direct methods using SHELXTL12 and were refined on F2 by a full-matrix
Synthesis of Complex HL1 NO3, 1. Complex 1 was obtained by
3
adding 0.2 mL of 69% nitric acid to 10 mL of methanolic solution of L1
(272.26 mg, 1 mmol). After the addition of acid, the clear solution was
filtered and kept for crystallization at room temperature. Yellowish
crystals suitable for X-ray crystallography were obtained after 2-3 days.
Yield of 1: 62%; 1H NMR (DMSO-d6, 500 MHz) δ (ppm) 4.48 (d, 2H),
7.15 (t, 1H, -NH), 7.62 (d, 2H), 7.96 (t, 1H), 8.13 (d, 2H), 8.41 (1H),
8.77 (1H), 8.81 (s, 1H), 9.62 (s, -NH). 13C NMR (125 MHz, DMSO-d6) δ
(ppm) 40.25, 117.15, 125.08, 126.40, 139.52, 140.73, 141.85, 143.35,
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dx.doi.org/10.1021/cg101595n |Cryst. Growth Des. 2011, 11, 1642–1650

Crystal Growth & Design
ARTICLE
Table 1. Crystallographic Parameters of Complexes 1-6
parameters
1
2
3
4
5
6
formula
C
13H13N5O6
C13H13ClN4O7
372.72
C26H26F6N8O6Si
344.32
C27H21F10N9O9
805.53
C14H10F5N3O3
363.25
needle
C24H14F10N6O6S
704.47
block
M
335.28
block
crystal habit
crystal system
space group
a/Å
needle
block
block
triclinic
P1
triclinic
P1
triclinic
P1
triclinic
P1
orthorhombic
Pna21
orthorhombic
P212121
7.7890(10)
18.282(2)
18.558(2)
90
8.256(10)
9.084(10)
10.619(10)
103.73(10)
102.17(10)
102.31(10)
726.62(14)
2
8.586(5)
10.343(6)
10.905(11)
113.510(10)
108.280(10)
99.450(10)
795.3(10)
2
6.3850(10)
7.8280(10)
14.914(2)
104.360(10)
100.100(10)
93.240(10)
707.03(17)
2
10.198(2)
10.250(2)
16.458(3)
87.780(10)
77.010(10)
72.990(10)
1602.3(5)
2
10.9560(10)
17.7010(10)
7.4980(10)
90
b/Å
c/Å
R/ꢀ
β/ꢀ
γ/ꢀ
V/Å3
90
90
90
90
1454.1(2)
4
2642.6(5)
4
Z
Dc/g cm-3
μ/mm-1
2θ range [ꢀ]
T/K
1.532
1.556
1.617
1.670
1.659
1.771
0.124
0.287
0.182
0.163
0.160
0.249
50.00
45.00
50.00
50.00
49.96
49.88
100(2)
348
100(2)
384
100(2)
100(2)
816
100(2)
736
100(2)
1416
F(000)
354
λ/Å
0.7107
0.154/-0.206
8465
0.7107
0.7107
0.7107
0.7107
0.127/-0.185
12548
0.7107
0.203/-0.260
14092
min/max/e Å-3
total reflections
unique reflections
reflections used
R1, I > 2σ(I)
wR, I > 2σ(I)
0.286/-0.364
3063
0.196/-0.318
6850
0.251/-0.282
24216
2545
1969
2496
8920
2514
4398
2292
1515
2312
5998
2411
3940
0.0313
0.0910
0.0511
0.0278
0.0439
0.0239
0.0609
0.0328
0.0710
0.1409
0.0736
0.0977
Scheme 2. Syntheses of Ureido-Pyridyl Ligands, L1 and L2
least-squares technique using the SHELXL-9713 program package.
Graphics were generated using PLATON14 and MERCURY 2.3.15 In
all cases, non-hydrogen atoms were treated anisotropically, and all of
the hydrogen atoms attached with carbon atoms were geometrically
fixed. Hydrogen atoms attached with nitrogen atoms are located in
electron Fourier map.
respectively. The synthetic procedures have been described in
Scheme 2. Both the ligands, L1 and L2, can be considered as good
candidates for the investigation of anion binding with various
polyatomic-anions, as they have two different electron withdrawing
substitutions in addition to a urea moiety as well as the pyridyl-N in
two different positions (3-N and 4-N). Attached electron with-
drawing groups and protonation sites in the ligand architecture can
presumably play a role in changing the binding nature of the ligand
toward anions as well as the variations in the two-dimensional
molecular arrangement, upon protonation of the pyridyl group. We
have attempted to isolate the protonated salt of L1 and L2 with
anions of various geometries under different media of crystallization.
We are able to isolate only these six complexes1-6 as single crystals
’ RESULTS AND DISCUSSION
Syntheses. We have designed and synthesized two different
ureido-pyridyl ligands, 1-(4-nitro-phenyl)-3-pyridine-3-ylmethyl-
urea, L1 and 1-pentafluorophenyl-3-pyridine-4-yl-urea, L2, with nitro-
phenyl and pentafluorophenyl as electron withdrawing substitutions,
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Crystal Growth & Design
ARTICLE
Table 2. Characteristic Hydrogen Bonds Observed in the Complexes 1-3
complex name
D-H
A
H
A/Å
D
A/Å
—D-HA/ꢀ
symmetry code
3 3 3
3 3 3
3 3 3
1
N1-H1A O6
1.98(2)
2.14(2)
1.99(2)
2.55(2)
2.42(2)
2.44(2)
2.890(2)
3.019(2)
2.877(2)
3.303(2)
3.264(2)
3.237(2)
164.4(2)
170.6(1)
178.1(1)
136.1(1)
147.4(1)
140.6(1)
1 - x, 1 - y, 2 - z
1 - x, 1 - y, 1 - z
1 - x, 1 - y, 1 - z
1 þ x, y, z
3 3 3
N2-H2A O4
3 3 3
N3-H3A O5
3 3 3
C1-H1 O5
3 3 3
C3-H3 O2
1 - x, -y, -z
3 3 3
C5-H5 O4
1 þ x, 1 þ y, z
3 3 3
2
N1-H11 O3
2.07(7)
2.23(5)
2.12(6)
2.58(5)
2.56(5)
2.44(6)
2.793(8)
2.988(7)
2.939(7)
3.257(7)
3.243(8)
3.290(8)
148(6)
175(5)
173(5)
134(5)
137(4)
159(5)
-x, 1 - y, 1 - z
-1 þ x, y, z
3 3 3
N2-H21 O4
3 3 3
N3-H31 O5
-1 þ x, y, z
3 3 3
C1-H1 O5
3 3 3
C3-H3 O2
-1 þ x, -1 þ y, -1 þ z
-1 þ x, y, -1 þ z
3 3 3
C5-H5 O1
3 3 3
3
N1-H1A F3
1.82(2)
2.34(2)
2.19(2)
2.09(2)
2.34(2)
2.27(2)
2.43(2)
2.49(2)
2.741(1)
3.056(1)
2.926(1)
2.878(1)
3.113(2)
3.175(2)
3.181(20
3.415(2)
168.5(2)
147.0(2)
149.5(2)
158.8(2)
138.4(1)
161.7(1)
136.4(1)
159.7(1)
-1 þ x, y, z
3 3 3
N2-H2A F2
x, 1 þ y, z
3 3 3
N2-H2A F1
1 - x, 1 - y, 1 - z
x, 1 þ y, z
3 3 3
N2-H3A F2
3 3 3
C1-H1 F1
-1 þ x, y, z
3 3 3
C5-H5 F3
-x, 1 - y, 1 - z
1 - x, 1 - y, -z
2 - x, 2 - y, -z
3 3 3
C3-H3 O2
3 3 3
C12-H12 O3
3 3 3
Figure 1. View depicting the interactions of the NO3- ion with [HL1]þ in complex 1.
2
suitable for single crystal X-ray analysis. The detailed structural
analyses of these complexes are described below.
established through R2 (8) N-H...O hydrogen bond with the
hydrogen bonding parameters: N2-H2A O4 (N2 O4 =
3 3 3 3 3 3
Binding of Polyatomic Anions with [HL1]þ. Protonated salts
of L1 with HNO3, HClO4, and HF have been isolated as
complexes 1, 2, and 3, respectively. All the crystals have been
characterized by single crystal X-ray crystallography (Table 1).
The structural analysis revealed that the anions coordinated with
the receptors via various hydrogen bonding interactions. De-
tailed hydrogen bonding interactions of the complexes 1, 2, and 3
are given in Table 2.
3.019 Å, —N2-H2A O4 = 171ꢀ) and N3-H3A O5
3 3 3 3 3 3
(N3 O5 = 2.877 Å, and —N3-H3A O5 = 178ꢀ). In
3 3 3
3 3 3
addition to the hydrogen bonding interactions with urea moieties,
the coordinated NO3- ion is in strong hydrogen bonding interac-
tions with pyridinium -NH protons and pyridinium -CH protons
as shown in Figure 1. The detailed hydrogen bonding interactions
are as follows: N1-H1A O6(N1 O6 = 2.890 Å, and —N1-
3 3 3
3 3 3
H1A O6 = 164ꢀ), C1-H1 O5 (C1 O5 = 3.303 Å, and
3 3 3 3 3 3 3 3 3
Binding of NO3 to [HL1]þ in Complex 1. Complex 1 was
-
—C1-H1 O5 = 136ꢀ), and C5-H5 O4 (C5 O4 =
3 3 3
3 3 3
3 3 3
3.237 Å, and —C5-H5 O4 = 141ꢀ). A complete list of
crystallized in P1 space group and the asymmetric unit contains
3 3 3
one molecule of L1 and one nitrate anion. Structural analysis
hydrogen bonding interactions of complex 1 is given in Table 2.
Thus, in complex 1, the NO3- ion is coordinated with three
-
revealed that one NO3 ion is coordinated with three of the
protonated L1 units via strong N-H...O and C-H O inter-
units of HL1 units and is stabilized by two N-H O interac-
3 3 3
3 3 3
actions as shown in Figure 1. The primary interactions are
tions from urea, two N-Hpy O and C-H O interactions
3 3 3
3 3 3
1645
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Crystal Growth & Design
ARTICLE
Figure 3. MERCURY diagram depicting the interactions of the ClO4
ion with three units of [HL1]þ in complex 2.
-
-3 3 3
Figure 2. View showing the NO3
NO3- interactions and the hydro-
gen bonding interactions of NO3 to the protonated receptor unit in
with oxy-acids such nitric and perchloric acids yielded complexes 1
and 2 in which the corresponding anions were bound with the urea
functionality of the ligand via the same binding topology.
complex 1.
Binding of SiF6 to [HL1]þ in Complex 3. Complex 3
2-
from pyridinium units of two different ligands. Thus, the overall
coordination number of the NO3- ion is six in 1. Further, such
quadrate units are interconnected through NO3
crystallized in triclinic P1 space group. Structural analysis re-
vealed that one SiF62- ion is hydrogen bonded with four units of
protonated receptor L1 via N-H...F hydrogen bonds as shown in
-
-
NO3
3 3 3
interactions (O6 O6, 2.77 Å) in two dimensions as shown
3 3 3
in Figure 2. It is important to mention that NO3
2-
Figure 4a. Two of the L1Hþ units are in coordination with SiF62-
-
-
NO3
3 3 3
through their two urea moieties and four F atoms of SiF6
through the formation of cyclic N-H...F hydrogen bonds,
whereas remaining two F atoms are in hydrogen bonding
interaction with the pyridinium hydrogen of two other L1Hþ.
Detailed hydrogen bonding interactions are as follows:
N1-H1A F3 (N1 F3 = 2.741(1) Å, —N1-H1A F3 =
interactions in the solid state are quite interesting, and indeed it is
known from the literature that NO3
have a great importance in describing the structural features of
-
-
NO3 interactions
3 3 3
the corresponding salts.16
Upon protonation of the pyridine nitrogen atom, the aryl-CH
protons of the pyridine units become more acidic due to the positive
charge in the pyridinium ring, and hence the aryl -CH protons are
more prone to form hydrogen bonding interactions with NO3- ion.
Though the receptor possesses only one urea unit, to satisfy the
number of coordination the nitrate anion interacted with two other
protonated receptor molecules. Other than urea functionality, the
protonated L1 possesses pyridinium -NH and -CH protons adjacent
to a protonated pyridyl nitrogen center as a hydrogen bonding
element which allow six coordination to the anion.
3 3 3
3 3 3
3 3 3
168.5(2)ꢀ), N2-H2A F1 (N2 F1 = 2.926(1) Å, —N2-
3 3 3 3 3 3
H2A F1 = 149.5(2)), N3-H3A F2 (N3 F2
3 3 3 3 3 3 3 3 3
=
2.878(1)Å, —N3-H3A F2 = 158.8(2)), and C1-H1
3 3 3
3 3 3
F1 (C1 F1 = 3.175(2) Å, —C1-H1 F1 = 138.4(1)).
3 3 3
3 3 3
Complete list of hydrogen bonding interactions of complex 3
are given in Table 2. Thus, one SiF62- anion was strongly bound
with four L1Hþ ligands leading to the formation of a square as
depicted in Figure 4b. Further, such adjacent squares are
aggregated to yield a two-dimensional sheet and the sheets are
stacked along the a-axis in three dimensions.
-
Binding of ClO4 to [HL1]þ in Complex 2. Complex 2 is
crystallized in triclinic space group P1. Crystal structure analysis
shows that the asymmetric unit contains one protonated ligand,
[HL1]þ, and a ClO4- anion. Structure analysis revealed that one
ClO4- ion is coordinated with three of the protonated L1 units
Binding of Polyatomic Anions with [HL2]þ. Binding of
polyatomic anions have also been performed with the ureido-
pyridyl ligand L2 which possesses a strong electron withdrawing
pentafluorophenyl group without any spacer. Several attempts
have been made to isolate the protonated salts of L2 under
different mediums of crystallization. However, we could isolate
only HNO3, CH3COOH, and H2SO4 complexes of L2 as
complexes 4, 5, and 6, respectively, as crystals suitable for single
crystal X-ray analysis. All these complexes have been character-
ized structurally and anions are coordinated with the protonated
receptor units via various hydrogen bonding interactions. De-
tailed hydrogen bonding interactions are given in Table 3.
Binding of NO3- to [HL2]þ in Complex 4. Protonation of L2
with HNO3 in a solution of dimethylformamide (DMF) afforded
complex 4 as colorless block crystals which are suitable for single
crystal X-ray crystallographic analysis. Solid state structure of 4
revealed that the complex crystallized in triclinic P1 space group,
and there are two protonated molecules of L2 (L2Hþ), two
nitrate anions, and one DMF molecule present in the asymmetric
via strong N-H O and C-H O interactions as shown in
3 3 3
3 3 3
Figure 3. Further, the primary interactions are established
through R2 (8) N-H...O hydrogen bonding interactions with
2
urea -NH protons with following bonding parameters as
observed in the case of complex 1: N2-H21 O4
3 3 3
(N2 O4 = 2.9852 Å, and —N2-H21 O4 = 173ꢀ), N3-
3 3 3 3 3 3
H31 O5 (N3 O5 = 2.9344 Å, and —N3-H31 O5 =
3 3 3 3 3 3 3 3 3
173ꢀ), C1-H1 O5 (C1 O5 = 3.257 Å, —C1-H1 O5 =
3 3 3 3 3 3 3 3 3
133.85ꢀ) and C10-H10 O7 (C10 O7 = 3.286 Å, —C10-
3 3 3
3 3 3
H10 O7 = 125.29ꢀ). A complete list of hydrogen bonding
3 3 3
interactions of complex 2 is given in Table 2.
Here the ClO4- ion is hydrogen bonded with receptor units by
four hydrogen bonding interactions (two from urea -NH protons
and another two from pyridinium -CH protons of two different
ligands). The ClO4- ion interacts with the pyridinium -NH protons
as observed in the case of 1. Thus, the cocrystallization of ligand L1
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Crystal Growth & Design
ARTICLE
Figure 4. (a) MERCURY diagram depicting the N-H F and C-H F interactions of the SiF62- ion with four units of [HL1]þ in complex 3 and
3 3 3
3 3 3
(b) the three-dimensional stacked sheets formed by the aggregation of adjacent molecular squares.
Table 3. Characteristic Hydrogen Bonds Observed in the Complexes 4-6
complex name
D-H
A
H
A/Å
D
A/Å
—D-H A/ꢀ
symmetry code
3 3 3
3 3 3
3 3 3
3 3 3
4
N1-H1 O3
1.98(2)
1.99(2)
2.09(2)
1.93(2)
2.01(2)
2.02(2)
2.41(2)
2.43(2)
2.55(2)
2.48(2)
2.48(2)
2.51(2)
2.54(2)
2.57(2)
2.839(2)
2.823(2)
2.914(2)
2.826(2)
2.859(2)
2.836(2)
3.153(2)
3.190(2)
3.367(2)
3.240(2)
3.222(2)
3.261(2)
3.31292)
3.424(2)
168.2(2)
166.6(2)
173.9(2)
176.8(1)
171(2)
1 - x, 1 - y, 1 - z
1 - x, 2 - y, 1 - z
1 - x, 2 - y, 1 - z
-1 þ x, y, z
3 3 3
N2-H21 O2
3 3 3
N3-H31 O1
3 3 3
N4-H41 O4
3 3 3
N5-H51 O6
-1 þ x, 1 þ y, z
-1 þ x, 1 þ y, z
3 3 3
N6-H61 O5
171.9(2)
133.5(2)
135.6(1)
144.3(1)
137.3(1)
148.2(1)
136.7(1)
137.6(1)
140.9(2)
3 3 3
C3-H3 O1
3 3 3
C3-H3 O7
3 3 3
C4-H4 O6
1 - x, 1 - y, -z
x, 1 þ y, z
-x, 1 - y, -z
-x, 1 - y, -z
-1 þ x, 1 þ y, z
3 3 3
C5-H5 O2
3 3 3
C13-H13 O2
3 3 3
C13-H13 O3
3 3 3
C14-H14 O6
3 3 3
C26-H26 O4
3 3 3
5
N1-H1A O3
1.64(2)
1.81(2)
2.04(2)
2.48(2)
2.55(2)
2.56(2)
2.24(2)
2.609(2)
2.681(2)
2.858(2)
3.456(2)
3.36(2)
169.8(2)
167(2)
1/2 - x, 1/2 þ y, 1/2 þ z
3/2 - x, 1/2 þ y, 1/2 þ z
3 3 3
N2-H2A O2
3 3 3
N3-H3A O3
178(3)
3 3 3
C1-H1 F2
171.9(2)
150.1(5)
134.0(1)
141.2(1)
3 3 3
C5-H5 F1
3 3 3
C4-H4 O2
3.233(2)
3.005(2)
3 3 3
C5-H5...O1
-1/2 þ x, 1/2 - y, z
-x, -1/2 þ y, 1/2 - z
6
N1-H1A O5
1.61(3)
2.06(3)
2.01(3)
1.80(3)
2.00(3)
1.84(3)
2.48
2.617(3)
2.897(3)
2.776(3)
2.750(3)
2.912(3)
2.732(3)
3.247(3)
3.231(3)
3.312(4)
3.386(4)
175(2)
170(3)
177(3)
163(3)
166(3)
179(4)
139
3 3 3
N2-H2A O3
3 3 3
N3-H3A O4
3 3 3
N4-H4A O4
1 - x, -1/2 þ y, 1/2 - z
1 - x, 1/2 þ y, 1/2 - z
1 - x, 1/2 þ y, 1/2 - z
1/2 - x, -y, -1/2 þ z
3 3 3
N5-H5A O3
3 3 3
N6-H6A O6
3 3 3
C1-H1 O2
3 3 3
C16-H16 O3
2.47
139
3 3 3
C13-H13 F5
2.40
167
1 - x, -1/2 þ y, 1/2 - z
1 - x, -1/2 þ y, 1/2 - z
3 3 3
C17-H17 F10
2.46
171
3 3 3
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Crystal Growth & Design
ARTICLE
Figure 5. (a) MERCURY diagram depicting the N-H O and C-
3 3 3
-
-
H
O interactions of the NO3
NO3 dimer with four units of
Figure 6. Two-dimensional sheets formed by the molecular tapes of
L2Hþ and NO3 observed in complex 4. Interactions of DMF molecules
with the clefts are omitted for clarity.
3 3 3
[HL1]þ in complex 4.
3 3 3
unit. The molecular packing analysis shows that L2Hþ is
coordinated with a NO3- ion through cyclic N-H O hydro-
3 3 3
gen bonding interactions. In addition to the hydrogen bonding
with urea -NH protons, the coordinated NO3- ion is in strong
interaction with -NH protons as well as -CH protons of
pyridinium moieties. Detailed hydrogen bonding interactions
and bond parameters are as follows: N1-H1 O3 (N1
3 3 3
3 3 3
3 3 3
O3 = 2.839(2) Å, —N1-H1 O3 = 168.2(2)), N2-H21
3 3 3
O2 (N2 O2 = 2.823(2) Å, —N2-H21 O2 = 2.823(2) Å),
3 3 3
3 3 3
N3-H31 O1 (N3 O1 = 2.914(2) Å, —N3-H31
3 3 3
3 3 3
3 3 3
O1 = 173.9(2)ꢀ), N4-H41 O4 (N4...O4 = 2.826(2) Å,
3 3 3
—N4-H41...O4 = 176.8(1)ꢀ), N5-H51 O6 (N5 O6 =
3 3 3
3 3 3
3 3 3
2.859(2) Å, —N5-H51 O6 = 171(2) ꢀ), N6-H61 O5
3 3 3
(N6 O5 = 2.836(2) Å, —N6-H61 O5 = 171.9(2) ꢀ). In
3 3 3
3 3 3
addition to the above-described conventional hydrogen bonding
interactions, in complex 4, NO3 is also involved in C-H...O
-
interactions with pyridinium moieties. A complete list of hydro-
gen bonding interactions and the bond parameters are given in
Table 3. As observed in the case of complex 1, in complex 4 also,
-
the nitrate ion exists as a NO3
NO3- dimer (Figure 5) that
3 3 3
leads to a quadrate unit (Figure 6). The adjacent quadrate units
are interconnected through N-H O hydrogen bonds formed
3 3 3
between the pyridinium moiety of L2Hþ and the nitrate anion to
yield a two-dimensional molecular tape along the b-axis. Further,
the tapes are interconnected through DMF molecules, which are
entrapped in the clefts formed by the molecular tape, with the
Figure 7. (a) Hydrogen bonding interactions of AcO- ion with the
protonated receptor units of L2 in complex 5. (b) AcO- assisted
formation of a zigzag 1-D network in complex 5.
help of weak interactions such as C-F π formed between the
3 3 3
Binding of CH3COO- to [HL2]þ in Complex 5. Complex 5
crystallized in Pna21 orthorhombic space group as colorless
single crystals suitable for X-ray analysis by treating L2 with
acetic acid in a solution of CH3OH. The asymmetric unit of the
complex contains one protonated unit of L2Hþ and one
CH3COO-. The structural analysis revealed that the acetate
pentafluorophenyl moiety and the DMF molecule which leads to
a two-dimensional planar sheet as shown in Figure 6. The solvent
molecules act as connectors of the tapes to yield two-dimensional
sheets. It is worth mentioning that the hydrogen bonding pattern
and the crystal packing arrangements of the complex 4 resemble
that of 1. However, the fluorine substitutions on L2 do not have
much influence on changing the hydrogen bonding pattern in the
complex but a little on the molecular packing arrangement. The
one-dimensional tapes in complex 4 are connected through the
solvent molecules present in clefts, and similar types of molecular
tapes in complex 1 are directly connected to each other through
anion is bound with L2Hþ via N-H O interactions of the
3 3 3
urea moiety (Figure 7). The detailed hydrogen bonding inter-
actions and the bond parameters are as follows: N1-H1A O3
3 3 3
(N1 O3 = 2.609(2) Å, —N1-H1A O3 = 169.8(2)ꢀ),
3 3 3 3 3 3
N2-H2A O2 (N2 O2 = 2.681(2) Å, —N2-H2A
3 3 3 3 3 3
3 3 3
weak C-H O hydrogen bonds formed between the tapes
O2 = 167(2)) and N3-H3A O3 (N3 O3 = 2.858(2) Å,
3 3 3 3 3 3
3 3 3
making use of the NO3- present in the ligand.
—N3-H3A O3 = 178(3)). A complete list of hydrogen
3 3 3
1648
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Crystal Growth & Design
ARTICLE
—N1-H1A O5 = 175(2)ꢀ), N2-H2A O3 (N2 O3 =
3 3 3 3 3 3 3 3 3
2.897(3) Å, —N2-H2A O3 = 170(3)ꢀ), N3-H3A
3 3 3
3 3 3
O4 (N3 O4 = 2.776(3) Å, —N3-H3A O4 = 177(3)ꢀ),
3 3 3 3 3 3
N3-H3A O4 (N3 O4 = 2.776(3) Å, —N3-H3A O4 =
3 3 3 3 3 3 3 3 3
177(3)ꢀ), N4-H4A O4 (N4 O4 = 2.750(3) Å, —N4-
3 3 3 3 3 3
H4A O4 = 163(3)ꢀ),N5-H5A O3(N5 O3 = 2.912(3) Å,
3 3 3 3 3 3 3 3 3
—N5-H5A O3 = 166(3) ꢀ), N6-H6A O6 (N6 O6 =
3 3 3
3 3 3
3 3 3
2.732(3) Å, —N6-H6A O6 = 179(4) ꢀ). Other than these
3 3 3
convention hydrogen bonding interactions, the coordinated sulfate
is also involved in C-H...O interactions with the pyridinium units. A
complete list of hydrogen bonding interactions along with bond
parameters is given in Table 3. Further, this kind of adjacent
spherical unit is connected through a similar type of N-H
O
3 3 3
hydrogen bond, where the SO42- anion is bound with the remain-
2
ing urea moieties through R2 (8) and two other pyridinium units
forming a similar type of hydrogen bonding environment, to yield a
three-dimensional network as shown in Figure 9. Thus, each
spherical unit contains a SO42- anion embedded around the four
units of L2Hþ through the strong N-H O hydrogen bonds.
3 3 3
’ CONCLUSION
Figure 8. Hydrogen bonding interactions of SO42- in complex 6.
In summary, we have shown the coordination of polyatomic
anions of various geometries (planar, tetrahedral, and octahedral)
with two new ureidopyridyl ligands in their protonated forms.
Detailed structural analysis of these complexes clearly demonstrates
that the anion binding occurs mostly via urea -NH, pyridinium -
NH, and -CH hydrogen adjacent to the pyridinium moiety. In all
cases, the primary binding of these polyatomic anion always occurs
2
at the urea moiety, through the R2 (8) recognition patterns formed
by strong N-H O hydrogen bonds. Thus, neither the substit-
3 3 3
uents/topology of the receptor nor the geometry of the anions has
influence on the primary binding motif of anions with receptors of
this category.
’ ASSOCIATED CONTENT
S
Supporting Information. NMR spectra and crystallo-
b
graphic information file. This material is available free of charge
via the Internet at http://pubs.acs.org.
’ AUTHOR INFORMATION
Corresponding Author
*E-mail: icpg@iacs.res.in; fax: (þ91) 33-2473-2805.
Figure 9. Packing diagram showing the three-dimensional network
formed by SO42- in complex 6.
’ ACKNOWLEDGMENT
bonding interactions of complex 5 is given in Table 3. Such
adjacent dimeric units are held together by N-H...O hydrogen
bonds formed between the pyridinium moiety of [HL2]þ
and acetate anion to form a one-dimensional zigzag chain
(Figure 7b).
P.G. gratefully acknowledges the Department of Science and
Technology, New Delhi, India, for financial support (Grant SR/
S1/IC-16/2008). The single-crystal data of all the complexes
were collected in the DST funded National single crystal X-ray
facility at the Department of Inorganic Chemistry, IACS. M.A.
acknowledges CSIR, India, for the award of SRF.
Binding of SO4 to [HL2]þ in Complex 6. The asymmetric
-
unit of the complex 6 contains two protonated units of [HL2]þ
and one sulfate (SO42-) anion as revealed from its crystal
structure. The structural analysis of the complex shows that
one SO42- anion is bound with four units of L2Hþ as shown in
Figure 8. Among the four receptor units two are connected
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1649
dx.doi.org/10.1021/cg101595n |Cryst. Growth Des. 2011, 11, 1642–1650

Crystal Growth & Design
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