Lower rim substituted p-tert-butyl calix[4]arene; Part 14. Synthesis, structures and binding studies of calix[4]arene thioamides

Article abstract of DOI:10.1007/s10847-010-9735-2

A number of p-tert-butylcalix[4]arene thioamides were synthesized and characterized by ¹H-NMR and elemental analysis. Compounds 1-5 are O-substituted derivatives with -CH₂-C(=S)-N-X groups, where NX = morpholidyl, NEt₂, NH

Full text of DOI:10.1007/s10847-010-9735-2

J Incl Phenom Macrocycl Chem (2010) 68:75–83
DOI 10.1007/s10847-010-9735-2
ORIGINAL ARTICLE
Lower rim substituted p-tert-butyl calix[4]arene; Part 14.
Synthesis, structures and binding studies of calix[4]arene
thioamides
•
Maria Bochenska Joanna Kulesza
•
´
Jarosław Chojnacki Franc¸oise Arnaud-Neu
•
•
´
Veronique Hubscher-Bruder
Received: 25 September 2009 / Accepted: 10 January 2010 / Published online: 4 February 2010
Ó Springer Science+Business Media B.V. 2010
Abstract A number of p-tert-butylcalix[4]arene thioam-
1
ides were synthesized and characterized by H-NMR and
Introduction
elemental analysis. Compounds 1–5 are O-substituted
derivatives with –CH2–C(=S)–N–X groups, where NX =
morpholidyl, NEt2, NHC2H4Ph, NHCH2Ph and NHEt,
respectively. The X-ray structures of the ligands 1, 3, 5 and
of the complex 3ꢀPb(ClO4)2, (compound 6), are presented
and their slightly distorted cone conformation is estab-
lished. The influence of the nature of the thioamide func-
tions (secondary or tertiary) on the extractability of some
selected metal cations was investigated. Whereas all these
calixarenes show the highest extraction level for Ag?,
tertiary thioamides are more efficient extractants for Pb2?
than secondary thioamides.
High impact is put nowadays to control the level of toxic
heavy metals, like lead, cadmium, copper or mercury, in
natural waters, which may cause great risk to human
health. Our objective in this work was to design ligands
possessing the ability of binding these metal cations. Pre-
vious studies have shown that the versatile ionophoric
properties of chemically modified calixarenes depend
greatly on the nature of the different substituents attached
to the calixarene scaffold [1–6]. The introduction of soft
donor atoms such as phosphorus or sulphur atoms into
calix[4]arene substituents has been shown to promote their
complexing ability towards transition and heavy metal ions
[7]. For example the replacement of the amide carbonyl
oxygen atoms of amide groups by sulphur atoms leading to
thioamides [8, 9]. The X-ray crystal structure of the lead
complex of the p-tert-butylcalix[4]arene diethylthioamide
(2) showed that Pb2? was bound to the four ethereal oxy-
gen and the four thiocarbonyl sulphur atoms of the ligand
in the cone conformation.
Keywords p-tert-butylcalix[4]arene thioamides ꢀ
Synthesis ꢀ Crystal structure ꢀ Liquid–liquid extraction
This paper reports the synthesis and the characteriza-
tion of new calix[4]arene ligands appended with tertiary
(compound 1) and secondary thioamide moieties (com-
pounds 3–5). The X-ray structures of the free ligands 1,
3 and 5 and of the lead complex of 3 (compound 6) are
also presented. A first estimation of the binding proper-
ties of these compounds towards a selection of metal
ions (Na?, Ca2?, Cu2?, Zn2?, Pb2?, Ag? and Gd3?) has
been investigated by liquid–liquid extraction of the cor-
responding metal picrates from water into dichloro-
methane. The results have been compared to those
previously obtained with the p-tert-butylcalix[4]arene
diethylthioamide (2) [8, 9], which was re-synthesized in
this work.
´
M. Bochenska (&) ꢀ J. Kulesza
Department of Chemical Technology, Chemical Faculty, Gdansk
University of Technology, ul. Narutowicza 11/12, 80-233
Gdansk, Poland
e-mail: maria.bochenska@pg.gda.pl
J. Chojnacki
Department of Inorganic Chemistry, Gdansk University of
Technology, ul. Narutowicza 11/12, 80-233 Gdansk, Poland
J. Kulesza ꢀ F. Arnaud-Neu ꢀ V. Hubscher-Bruder
Laboratoire de Chimie-Physique, IPHC-DSA, UDS, CNRS,
ECPM, 25, rue Becquerel, 67087 Strasbourg Cedex 2, France
123

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J Incl Phenom Macrocycl Chem (2010) 68:75–83
Experimental
General
and then washed with water. The organic phase was dried
over MgSO4 and evaporated under reduced pressure. After
solvent removal the thioamides 1–5 were obtained as pale
brown or yellowish products after crystallization from the
CH2Cl2–MeOH mixture, or if necessary were purified by
means of silica gel chromatography. In the case of 1, 3 and 5
single crystals suitable for X-ray analysis were obtained
after few weeks or months of slow solvent evaporation. The
characteristics of the compounds 1–5 are presented below.
1H-NMR spectra were recorded in CDCl3 on a Varian
spectrometer (200 MHz). Elemental analysis was done on
Carlo Erba Instruments CHNS-O EA1108—Elemental
Analyzer. They both confirmed the structure and purity of
the compounds. The absorbances were measured on a
Shimadzu UV-2101 spectrophotometer.
25, 26, 27, 28-Tetrakis(thiomorpholidylmethoxy)-p-tert-
butylcalix[4]arene (1)
Chemicals
Organic reagents and solvents (dichloromethane, methanol
and toluene) were reagent grade and were used without
further purification. The starting materials, amides A–E, all
in the cone conformation, were obtained with good yields
(78–85%) and in some cases with excellent yields (91–98%)
by the procedure described before [3, 6]. Lawesson’s
Reagent was purchased from Aldrich. The metal picrates
were obtained according to the procedures described in the
C68H92O8N4S4 M.W. 1221.7, yield 59%, m.p. 240–245 °C,
1H-NMR (200 MHz, CDCl3): cone conformation d[ppm]:
1.08 (s, 36H, t-Bu); 3.16 (d, 4H, ArCH2Ar, J = 12.83 Hz);
3.48 (bs, 8H, Hmorph); 3.71–3.77 (m, 16H, Hmorph); 4.34
(bs, 8H, Hmorph); 4.88 (d, 4H, ArCH2Ar, J = 12.74 Hz);
5.19 (s, 8H, OCH2CO); 6.81 (s, 8H, ArH); Anal. calculated
for C68H92O8N4S4: C 66.79, H 7.58, N 4.58, S 10.47%;
Found: C 66.91, H 7.70, N 3.56, S 9.79%.
literature, starting from Na? hydroxide [10], Ca2?, Ni2?
,
Cu2?, Zn2?and Gd3? carbonates [11] and Pb2? acetate [12].
25, 26, 27, 28-Tetrakis(diethylthiocarbamoylmethoxy)-p-
tert-butylcalix[4]arene (2)
Pb(II)perchlorate trihydrate, 98%, was from Sigma–Aldrich.
Synthesis
C68H100O4N4S4, M.W. 1165.8, yield 68%, m.p. 212–
1
218 °C, H-NMR (200 MHz, CDCl3): cone conformation
The thioamides 1–5 were prepared according to the reac-
tion shown in Scheme 1, by the following procedure [13]:
The respective calix[4]arene amide (A, B, C, D or E),
(0.3 mmol) and the Lawesson’s Reagent (2.1 equiv.) dis-
solved in dry toluene were stirred overnight at 90 °C under
argon. After that time, the solvent was removed under
reduced pressure and the residue was dissolved in CH2Cl2
d[ppm]: 1.08 (s, 36H, t-Bu); 1.24 (t, 12H, NCH2CH3); 1.32
(t, 12H, NCH2CH3); 3.17 (d, 4H, ArCH2Ar,
J = 12.69 Hz); 3.61 (q, 8H, NCH2CH3); 3.98 (q, 8H,
NCH2CH3); 4.76 (d, 4H, ArCH2Ar, J = 12.21 Hz); 5.09 (s,
8H, OCH2CO); 6.79 (s, 8H, ArH); Anal. Calcd. for
C68H100O4N4S4 : C 70.06, H 8.65, N 4.81, S 11.0%; Found:
C 69.67, H 8.57, N 4.38, S 11.18%.
Scheme 1 The synthesis of
thioamides 1–5
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J Incl Phenom Macrocycl Chem (2010) 68:75–83
77
25, 26, 27, 28-Tetrakis(N-phenytylthiocarbamoylmethoxy)-
p-tert-butylcalix[4]arene (3)
isotropic model with Uiso(H) values fixed to be 1.5 times
Ueq of C atoms for CH3 or 1.2 times Ueq for CH2 and CH
groups. N–H were refined free with N–H distances fixed at
˚
0.88 A and Uiso(H) was refined free or fixed at 0.050.
C84H100O4N4S4, M.W. 1374.9, yield 64%, m.p. 233–
1
235 °C, H-NMR (200 MHz, CDCl3): cone conformation
Solutions and refinements were carried out using the
SHELX–97 program package [14].
d[ppm]: 1.08 (s, 36H, t-Bu); 2.99 (t, 8H, HNCH2CH2Ar);
3.11 (d, 4H, ArCH2Ar, J = 13.35 Hz); 4.06 (d, 4H,
ArCH2Ar, J = 13.56); 4.06 (m, 8H, HNCH2CH2Ar); 4.81
(s, 8H, OCH2CO); 6.73 (s, 8H, ArH); 7.22–7.26 (m, 20H,
ArHBenzyl); 8.70 (t, 4H, NH); Anal. Calcd. for
C84H100O4N4S4: C 74.29, H 7.42, N 4.13, S 9.43%;Found:
C 73.85, H 7.41, N 3.99, S 9.32%.
Details of X-ray diffraction data determination
Experimental diffraction data were collected on KM4CCD
kappa-geometry diffractometer, equipped with a Sapphire2
CCD detector. Enhanced X-ray MoKa radiation source
with a graphite monochromator was used. Determination of
the unit cells and data collection were carried out at 120 K.
Data reduction, absorption correction, space group deter-
mination, solution and refinement were made using Cry-
sAlis software package (Oxford Diffraction, 2008) [15].
Single frame exposure time was adjusted to obtain reliable
data for crystals of poor scattering power. Nevertheless,
this parameter could not be set longer than 90 s due to
serious ice-forming problems encountered.
25, 26, 27, 28-Tetrakis(N-benzylthiocarbamoylmethoxy)-p-
tert-butylcalix[4]arene (4)
C80H92O4N4S4, M.W. 1301.9, yield 69%, m.p. 191–194 °C,
1H-NMR (200 MHz, CDCl3): cone conformation d[ppm]:
1.06 (s, 36H, t-Bu); 3.00 and 4.17 (d, 4H, ArCH2Ar, J =
13.18 Hz); 4.81 (s, 8H, OCH2CO); 4.97 (d, 8H, HNCH2Ar);
6.66 (s, 8H, ArH); 7.26–7.35 (m, 20H, ArHBenzyl); 8.65 (t,
4H, NH); Anal. Calcd. for C80H92O4N4S4: C 73.81, H 7.12,
N 4.30, S 9.85%; Found: C 72.1, H 7.03, N 4.08, S 9.61%.
Details related with structure determinations for specific
samples are listed below.
Compound 1 One morpholine arm (starting from O1
atom) was found to be disordered over two positions,
occupied with probabilities: 0.766(10)/0.234(10). The
group was restrained to have identical C–C and C–N bond
lengths in both parts. Additionally, tert-butyl group C68,
C69, C70 was also found disordered over two positions
with occupation factors of 0.515(16)/0.485(16). Solvating
dichloromethane molecule was modeled as disordered over
two positions with occupation probabilities of 0.768(6)/
0.232(6). A second solvent molecule, present in the struc-
ture, was identified as methanol. Since it is disordered
(0.63/0.37) and located close to the inversion centre, it was
refined using isotropic displacement parameters and C–O
25, 26, 27, 28-Tetrakis(N-ethylothiocarbamoyl-
methoxy)-p-tert-butylcalix[4]arene (5)
C60H84O4N4S4, M.W. 1053.6, yield 72%, m.p. 263–264 °C,
1H-NMR (200 MHz, CDCl3): cone conformation d[ppm]:
1.09 (s, 36H, t-Bu); 1.24-1.33 (m, 12H, HNCH2CH3); 3.35
(d, 4H, ArCH2Ar, J = 12.9 Hz); 3.83-3.89 (m, 8H,
HNCH2CH3); 4.35 (d, 4H, ArCH2Ar, J = 12.9 Hz); 4.91 (s,
8H, OCH2CO); 6.82 (s, 8H, ArH); 8.60 (bs, 4H, NH); Anal.
Calcd. for C60H84O4N4S4: C 68.40, H 8.04, N 5.32, S
12.15%; Found: C 68.39, H 7.99, N 4.24, S 10.39%.
˚
distance restrained to d(C–O) = 1.435(1) A. We decided
Synthesis of the complex (6)
not to attribute hydrogen atoms to the molecule as it would
be very speculative.
Compound 3 (15 mg, 0.011 mmol) was dissolved in a
minimum amount of methylene chloride. Subsequently, a
solution of Pb(ClO4)2 trihydrate (0.044 mmol) in methanol
was added. The resultant solution was stored at room
temperature for several months yielding single crystals of 6
suitable for X-ray analysis; m.p. 273–274 °C.
Compound 3 The quality of the structure is not high due
to the low diffracting power of the specimen (all were
similar), but it is supported by similarity to the related
structure of its lead perchlorate complex 6. Most of the
atoms but sulphur atoms were refined in isotropic model in
order to keep the data to parameter ratio at reasonable
level. Conformation of the calixarene portion of the mol-
ecule can be analyzed with rather good confidence. A
single ethylphenyl group is disordered over two positions
with occupancies 0.543(7)/0457(7). This group was refined
with both parts constrained to have the same bond lengths
as the respective ordered groups. Additional restrains were
applied to assure proper shape of the phenyl groups. One
tertiary butyl group C59–C62 was modeled as disordered
X-ray structure analysis of compounds 1, 3, 5 and 6
General remarks
Structures of 1, 3, 5 and 6 were solved by direct methods
and all non-hydrogen atoms were refined with anisotropic
thermal parameters by full-matrix least squares procedure
based on F2. All hydrogen atoms were refined using
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J Incl Phenom Macrocycl Chem (2010) 68:75–83
X-ray diffraction data
over two positions 0.549(15)/0.451(15). A molecule of
water was found in a position that generates a hydrogen
bond of the N–HꢀꢀꢀO type.
Single crystals suitable for X-ray analysis were obtained
for the ligands 1, 3 and 5. The corresponding X-ray
molecular structures are presented in Figs. 1, 2, 3 and 4,
respectively. For calixarene 3 we managed to obtain
monocrystals of its complex with Pb(ClO4)2, which
allowed to determine also the structure of 6, presented in
Fig. 5.
Compound 5 One tert-butyl group C57–59 is disordered
over two positions with probabilities 0.60(3)/0.40(3). The
structure contains two solvent accessible voids of volume
3
˚
ca. 100 A . Program PLATON/SQUEEZE [16] revealed
that each void is occupied by disordered molecules pos-
sessing *17 e, probably methanol (see CIF file). The
electron density is smeared so much, that no well defined
position of a solvent could be found. The voids are placed
between the calixarene molecule, outside the cone.
Up to now, only two X-ray structures of calixarenes
substituted with thioamides were known. The first one
corresponds to a bis-substituted calix[4]arene with two
distal –CH2–C(=S)–NEt2 groups at the oxygen atoms of the
lower rim [18]. The authors noted that, in this structure, the
thioamide groups ‘‘are oriented in a divergent fashion’’.
The second structure is that of the complex of compound 2
with Pb(ClO4)2 [9]. The X-ray structure of the free
(uncomplexed) ligand 2 still remains unknown, which
hinders direct study on the conformational changes of the
ligand upon complexation. Such a possibility emerges now
in the case of the thioamide 3, bearing –CH2–C(=S)–NH–
C2H4Ph arms, for which both structures—of the free ligand
and of its lead perchlorate complex—are accessible.
Compound 6 Relatively strong scattering power of 6
crystals allowed to collect diffraction data with shorter
frame exposure times. It appeared necessary to apply
numerical absorption correction. The structure contains
3
˚
voids (of volume ca. 38 A ) at the calixarene cone. Search
with PLATON routines revealed no solvent molecules
trapped in the voids.
Extraction studies
Extraction studies were carried out according to the Pe-
dersen procedure [17] as follows:
Five milliliter of the aqueous solution of each metal
picrate and 5 mL of CH2Cl2 solution of respective
calix[4]arene, each of the same concentration 2.5 9 10-4
mol/L, were introduced into tubes with stoppers. After
10 min of vigorous shaking, followed by 30 min of mag-
netic stirring in a thermostated water bath at 20 0.1 °C,
the tubes were left standing for at least 30 min without
stirring, in order to complete phase separation. The per-
centage of cation extracted (%E) from water into dichlo-
romethane was determined from the absorbance (A) of the
picrate anion remaining in the aqueous phase after
extraction at kmax = 355 nm and from the absorbance (A0)
of a blank experiment without ligand.
%E ¼ 100ðA0 ꢁ AÞ=A0
Results and discussion
Synthesis
All the ligands studied were obtained with rather good
yield (59–72%) in a one-step synthesis, shown in
Scheme 1. This relatively easy synthetic route, using the
Lawesson’s Reagent, regarded as a convenient and efficient
thionating agent, led to the desired compounds. Their cone
conformation was confirmed by 1H-NMR spectroscopy
and, in the case of compounds 1, 3 and 5, by X-ray
structural analysis.
Fig. 1 Chemical structures of the studied ligands 1–5
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J Incl Phenom Macrocycl Chem (2010) 68:75–83
79
Fig. 2 Molecular structure of the compound 1 showing rings and
atoms numbering scheme. Hydrogen atoms, solvent molecules and
less-populated disorder parts are omitted
Fig. 4 Molecular structure of the compound 5 showing rings and
atoms numbering scheme. Hydrocarbonic H atoms and less-populated
disorder parts are omitted. Rings A and C are almost parallel—
dihedral angle 3.77°, dihedral angle between B and D: 83.55°. Some
intramolecular hydrogen bond of the N–HꢀꢀꢀO and N–HꢀꢀꢀS type can
be found
Fig. 3 Molecular structure of the compound 3. A view showing its
pinched cone conformation with two phenyl rings B and D almost
parallel, and rings A and C almost perpendicular, one intramolecular
N–HꢀꢀꢀS bond and two intramolecular N–HꢀꢀꢀO bond are presented.
The water molecule is linked by N2–H2ꢀꢀꢀO11 hydrogen bond. One
phenyl ring was omitted for clarity
Fig. 5 Molecular structure of the compound 6 (side view)
atoms (see Table 3). Rings A and C can be regarded as
almost parallel (dihedral angle between rings A–C is
9.76°), whereas the rings B and D are oriented at the angle
of 74.62° (Fig. 2). No solvent molecule was found inside
the cone. Strong hydrogen bonds are not found due to lack
of a good hydrogen donor group. Thiocarbonyl groups are
directed outside the center in positions optimal for weak
dispersion intermolecular interactions such as C–HꢀꢀꢀS
contacts. This is analogous to the conformation of the bis-
substituted thioamide calix[4]arene [18].
X-ray structure of 1
X-ray structural analysis of single crystals proved that
compound 1 adopts a pinched cone conformation, with
tert-butyl groups pitched away from the open cavity.
Conformation of the calixarene has been analyzed by cal-
culation of dihedral angles of the rings A–D to a reference
plane R passing through the methylene bridging carbon
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J Incl Phenom Macrocycl Chem (2010) 68:75–83
X-ray structure of 3
to be re-adjusted for coordination of a cation, which is
observed in the structure of 3ꢀPb(ClO4)2, described later
(see compound 6).
In the structure of compound 3, phenyl rings A and C are
practically parallel and ring B is almost perpendicular to
ring D. The dihedral angle between rings B and D is equal
to 89.47° and the angle between rings A and C is equal to
1.24°. Thiocarbonyl groups are directed outside the center
in positions optimal for intermolecular interactions. Their
spatial orientation arise mainly from intramolecular
N–HꢀꢀꢀO and N–HꢀꢀꢀS hydrogen bonds. Hydrogen bonds
formed in the structure are specified in Tables 1 and 2. It is
evident, that the conformation of the free ligand (3) needs
X-ray structure of 5
Rings A and C can be regarded as almost parallel (the
dihedral angle between A and C is 3.77°), whereas the
rings B and D form a dihedral angle of 83.55° (Fig. 4). The
lower rim conformation is influenced by N2–H2ꢀꢀꢀO1 and
weaker N1–H1ꢀꢀꢀS4 and N3–H3ꢀꢀꢀS2 intramolecular
hydrogen bonds (see Table 2). The solid may be regarded
Table 1 Crystal data and structure refinement details for compounds 1, 3, 5 and 6
Compound
1
3
5
6
Empirical formula
Molecular weight
Temperature (K)
C70H98Cl2N4O9S4
1338.7
C84H101N4O5S4
1374.93
C60H84N4O4S4
1053.6
C84H100Cl2N4O12PbS4
1764.0
120(2)
120(2)
120(2)
120(2)
´
˚
Wavelength (A)
0.71073
0.71073
0.71073
0.71073
Crystal system
Space group
Triclinic
Triclinic
Triclinic
Monoclinic
P21/c
P-1
P-1
P-1
´
˚
Unit cell dimensions (A)
a = 14.2270(8)
b = 14.2806(7
c = 20.2219(11)
a = 72.653(5)o
b = 78.609(5)o
c = 64.411(5)o
3525.7(3)
a = 13.6442(6)
b = 18.6204(8)
c = 18.7831(6)
a = 117.550(4)o
b = 98.043(3)o
c = 97.077(4)o
4092.2(3)
2
a = 13.3430(7)
b = 13.3822(7)
c = 18.3147(11)
a = 75.389(5)o
b = 82.708(5)o
c = 88.147(4)o
3138.9(3)
2
a = 17.7053(4)
b = 15.2829(3)
c = 31.3300(7)
a = 90o
b = 102.839(2)o
c = 90o
´
3
˚
Volume (A )
8265.6(3)
4
Z
2
Density (calculated, Mg/m3) 1.261
1.116
1.115
1.418
Absorption coefficient
(mm-1
F(000)
0.268
0.166
0.196
2.269
)
1432
1474
1136
3632
0.42 9 0.37 9 0.08 mm3
1.97–27.0o
Crystal size
0.43 9 0.32 9 0.26
1.98–26.00o
0.36 9 0.23 9 0.12
2.01–23.50o
0.36 9 0.28 9 0.14
2.20–25.50o
-14 \=h \=16,
-15 \=k \=16,
-22 \=1 \=22
21538
h range for data collection
Index ranges
-17 \=h \=17,
-17 \=k \= 14,
-24 \= 1 \=24
26614
-16 \=h \=15,
-21 \=k \= 22,
-22 \= 1 \=18
28507
-17 \=h \=22,
-11 \=k \=19,
-39 \=l \=34
34963
Reflections collected
Independent reflections
Completeness to theta (%)
Absorption correction
Refinement method
13818 [R(int) = 0.0621] 14391 [R(int) = 0.0853] 11574 [R(int) = 0.1040] 17768[R(int) = 0.0386]
26.00o 99.6
25.01o 99.7
25.50o 99.1
27.0o 98.4
None
None
None
Empirical
Full-matrix least-squares Full-matrix least-squares Full-matrix least-squares Full-matrix least-squares on
F2
on F2
on F2
on F2
Data/restrains/parameters
Goodness-of-fit on F2
13818/22/871
1.108
14391/54/475
1.220
11574/6/708
1.091
17768/0/964
0.936
Final R indices
[I [ 2sigma(I)]
Frame exposure (s)
R1 = 0.1044,
wR2 = 0.2462
R1 = 0.1598,
wR2 = 0.4013
R1 = 0.1091,
wR2 = 0.295
R1 = 0.0377,
wR2 = 0.0846
80
90
90
15
Largest diff. peak and hole 0.788 and -0.590
´
1.239 and -0.673
0.787 and -0.698
1.684 and -1.250
-3
)
˚
(eꢀA
123

J Incl Phenom Macrocycl Chem (2010) 68:75–83
81
˚
˚
˚
2.977(1) A with the mean of Pb–S 2.933(1) A. Pb–O bonds
are slightly longer than in previously described Pb-complex
of compound 2 [9]. Pb–S bonds in both complexes have
similar lengths. Torsion angles O–C–C–S in the chelating
fragments are more diverse in the present structure (–8.3(4);
43.3(4); 22.8(4); 9.1(4)° vs. 0(1); 17(1); 14(1); 2(1)° found in
[9]. Torsions angles Pb–S–C–N are more consistent than
found previously in the lead complex of 2 (–151.9(3);
–176.9(3); –169.8(3); –158.4(3)° vs. 139(3); 147(4); 153(3),
147(3)°). Nevertheless, one must remember those are the
angles which belong to different types of thioamides: sec-
ondary C(=S)NH–C2H4Ph (6) and tertiary C(=S)NEt2
(complex with 2).
Table 2 Geometry of hydrogen bonds (A, °) in structures of 3, 5 and
6 (D donor, A acceptor)
Compound Atom labels
D–H
HꢀꢀꢀA
DꢀꢀꢀA
Angle
(DHA)
3
N1–H1ꢀꢀꢀS4
N2–H2ꢀꢀꢀO11
N4–H4ꢀꢀꢀO3
N4–H4ꢀꢀꢀO4
N2–H2ꢀꢀꢀO1
N1–H1ꢀꢀꢀS4
N3–H3ꢀꢀꢀS2
N1–H1ꢀꢀꢀO9
N1–H1ꢀꢀꢀO10
0.86(4) 2.81(4) 3.568(13) 147(4)
0.88(4) 2.30(7) 3.11(2) 151(11)
0.89(4) 2.27(6) 2.967(9) 134(6)
0.89(4) 2.18(6) 2.684(9) 115(5)
0.89(3) 2.19(4) 3.006(6) 152(6)
0.85(3) 2.72(5) 3.368(6) 134(5)
0.87(3) 3.22(6) 3.726(7) 120(5)
0.88(4) 2.47(4) 3.124(5) 131(3)
0.88(4) 2.33(4) 3.206(5) 171(3)
5
6
The conformation of 6 is more regular (less pinched)
than that of the free ligand 3. Notable difference in con-
formation between the complex 6 and the ligand 3 is the
orientation of the aromatic rings B and D which in 6 are not
orthogonal anymore (dihedral angle of 52.7(9)o, Fig. 5).
The dihedral angles between the reference plane R and
rings A–D are quite uniform and are in the range of 62.9–
77.4o (see Table 3). In the related complex with 2 the
corresponding angles vary from 65 to 71o (after rescaling
as complement to 180o) [9]. Because the cone is less
N2–H2ꢀꢀꢀO8#1 0.88(4) 2.06(4) 2.940(4) 177(4)
N3–H3ꢀꢀꢀO11#2 0.88(6) 2.29(6) 3.147(5) 165(5)
N3–H3ꢀꢀꢀO12#2 0.88(6) 2.37(6) 3.053(5) 135(5)
N4–H4ꢀꢀꢀO7
0.95(4) 1.98(4) 2.878(4) 157(3)
Symmetry codes: #1: x, y ? 1, z; #2: x, -y ? 3/2, z ? 1/2
as a molecular crystal with no strong specific intermolec-
ular interactions.
´
3
˚
‘‘pinched’’ small void of volume 38 A is created inside the
cone. In contrast to earlier structure in 6 this void is not
occupied by solvent molecule. As expected, all the thio-
carbonyl sulphur atoms are directed towards the lead atom.
It follows that N–H groups, being hydrogen bond donors,
are oriented outside. The perchlorate anions are located in
positions optimal for intermolecular hydrogen bonding of
the N–HꢀꢀꢀO type. Some of the bonds (NH1 and NH3 as
donors) are bifurcated (see Fig. 6 and Table 2). Figure 6
also shows the clockwise twist of all four ethylphenyl
residues around the calixarene core. Clearly, because the
space group is centrosymmetric, both enantiomers are
present in the crystal.
X-ray structure of 6
This is the second example of the X-ray structure of a lead
perchlorate complex with a calix[4]arene thioamide deriv-
ative. The Pb-complex of the calix[4]arene diethyl thioamide
2, described in [9] contained (in average) half of a water
molecule trapped in the cone void. Both structures show
some similarities. The Pb2? cation in 6 is bound to four
ethereal oxygen atoms and four thiocarbonyl sulphur atoms.
Coordination polyhedron can be regarded as distorted
tetragonal (square) antiprism. The upper, oxygen ‘‘square’’ is
twisted by angle of ca 32° in relation to the lower sulphur
tetragon. As a measure of the twist we used the dihedral angle
between the planes defined by O1–Pb1–O3 and S1–Pb1–S3.
A similar twist angle (33°) was found in the structure of the
complex described in [9]. The Pb–O bond lengths are in the
Extraction
˚
range of 2.717(2)–2.751(2) A with the average of
˚
2.728(2) A whereas the Pb–S lay in the range of 2.869(1)–
Extraction data for thioamides 1–5 are given in Table 4. It
is clear that the thioamides studied here are inefficient
Table 3 Conformation of the calix fragment for compounds 1, 3, 5 and 6
1
3
5
6
˚
Reference plane Defining atoms, r.m.s deviation from the mean plane [A]
R
C17–C34–C51–C68, 0.0326 C21–C42–C63–C64 0.0977 C15–C30–C45–C60, 0.1836 C21–C42–C63–C64, 0.0255
Defining rings
Dihedral angles between the planes [°]
A-R
B-R
C-R
D-R
89.87 (0.12)
52.26 (0.10)
80.22 (0.12)
53.18 (0.13)
86.84(0.21)
46.83 (0.23)
85.14 (0.17)
42.68(0.29)
88.88 (0.15)
39.74 (0.20)
87.56 (0.16)
43.81 (0.10)
77.38(0.09)
62.93(0.09)
76.37(0.08)
64.35(0.09)
123

82
J Incl Phenom Macrocycl Chem (2010) 68:75–83
reported that calix[4]arene derivatives based on secondary
amide functions were inefficient in extraction of alkali and
alkaline earth picrates probably due to intra- and inter-
molecular hydrogen bonding combined to the high hydro-
philicity of the extracted complexes [19]. It has also been
proved that intramolecular hydrogen bonding in
calix[4]arenes bearing amino acids affected the extract-
ability towards metal ions [20]. According to literature
data, thioamides are weak hydrogen bond acceptors but
strong hydrogen bond donors in comparison to amides due
to the electronegativity of the sulphur atom [21]. Therefore,
secondary thioamides should have a strong ability to form
hydrogen bonds which is supported by the observation in
the crystal structure of ligand 3 of several intramolecular
hydrogen bonds (Table 2). In the structure of ligand 5 also
hydrogen bonds, of the N–HꢀꢀꢀO and N–HꢀꢀꢀS type, are
present. Tertiary thioamides have no N–H donor group, so
these interactions are not possible. Moreover, secondary
thioamides can interact with water molecules increasing
the affinity of the ligand for the aqueous phase. This fact
may explain, as with calix[4]arene amide derivatives, the
very low effectiveness of ligands 3, 4 and 5 for Pb2? and
other transition and heavy metal cations.
Fig. 6 Molecular structure of the compound 6 showing rings and
atoms numbering scheme. Hydrocarbonic H atoms are not shown. In
order to show hydrogen bonding network two neighbour symmetry
equivalents of perchlorate anions are drawn. Detailed description of
the bonds is given in Table 2
Table 4 Eextraction (%E)a of metal picrates (CM = 2.5 9 10-4 M)
with calix[4]arene-thioamides 1–5 (CL = 2.5 9 10-4 M) from water
into dichlormethane (organic to aqueous phase ratio o/a = 1,
T = 20 °C)
Conclusion
Mn?
1
2
3
4
5
The extraction results show the low affinity of calix[4]thio-
amides for alkali and alkaline earth metal ions and lanthanide
cations, contrary to most of the tertiary amides studied so far,
which are good extracting agents for these metal ions. This is
easily explained by the presence in thioamides, of soft sul-
phur atoms having a preference for soft cations like Ag?. The
results also show that this affinity is strongly dependent (as it
was previously shown in the amide series) on the nature of
the thioamide attached to the calixarene framework. The
dramatic drop in the extraction levels on going from the
tertiary to the secondary thioamide derivatives is certainly
due to the presence of donor N–H group enabling intramo-
lecular hydrogen bonding in these ligands and intermolec-
ular interactions with aqueous phase. The ionophoric
properties of compounds 1–5 in ion selective PVC-mem-
brane electrodes (ISEs) were also studied and are presented
in a separate paper [22].
Na?
Ca2?
Cu2?
Zn2?
Gd3?
Ag?
Pb2?
a
6.3
4.6
7b
B1
1.6
2.3
B1
B1
98.0
B1
2.0
2.8
2.9
B1
1.6
85.5
B1
B1
B1
1.9
B1
B1
92.1
B1
B1
19.0b
14.5
1.6
B1
4.8
B1
99.2
50.9
80.0b
56.0b
Values with uncertainties less than 5%
b
Data from [9]
extractants for alkali and alkaline earth metal ions and for
lanthanide(III) cations (at least for Gd3?). In contrast they
all extract almost quantitatively Ag? (%E C 80). The
extraction level of Pb2? depend strongly on the type of the
thioamide function: %E values of 51 and 56 have been
found with the tertiary thioamide derivatives 1 and 2,
whereas almost no extraction (%E B 1) could be noticed
with the secondary thioamide derivatives 3–5. Among the
transition metal ions, only Cu2? is fairly extracted by the
tertiary thioamide derivatives 1 and 2 (%E = 14.5 and
19.0, respectively). But again the secondary thioamide
derivatives were found to be inefficient with this kind of
cations. The influence of the amide type on the cation
binding has already been noticed [5, 19]. It has been
Supplementary material
Crystallographic data for the structures reported in this
paper 1, 3, 5 and 6 have been deposited with the Cambridge
Crystallographic Data Center as supplementary publication
No. CCDC 719145, CCDC 748376, CCDC 719144 and
CCDC 748377, respectively. Copies of the data can be
123

J Incl Phenom Macrocycl Chem (2010) 68:75–83
83
lead(II)and calix[4]arene amide–copper(II) complexes. J. Chem.
Soc. Perkin Trans. 2, 575–579 (1997). doi:10.1039/a605417j
10. Arnaud-Neu, F., Schwing-Weill, M.J., Ziat, K., Cremin, S.,
Harris, S.J., McKervey, M.A.: Selective alkali and alkaline earth
cation complexation by calixarene amides. New J. Chem. 15, 33–
37 (1991)
11. Aggarwal, R.C., Singh, N.K.: Synthesis and characterization of
some first row transition metal picrates. Def. Sci. J. 25, 153–158
(1975)
obtained free of charge on application to CCDC, 12 Union
Road, Cambridge CB2 1EZ, UK (Fax: (?44) 1223-336-
033; E-mail: deposit@ccdc.cam.ac.uk)
Acknowledgement Financial support from the Polish Ministry of
Higher Education and Science, grant No N204 274235, is gratefully
acknowledged.
12. Marcos, P.M., Ascenso, J.R., Segurado, M.A.P., Peirera, J.L.C.:
p-tert-butyldihomooxacalix[4]arene/p-tert-butylcalix[4]arene:
transition and heavy metal cation extraction and transport studies
by ketone and ester derivatives. J. Incl. Phenom. Macrocycl.
Chem. 42, 281–288 (2002)
13. No, K., Lee, J.H., Yang, S.H., Yu, S.H., Cho, M.H., Kim, M.J.,
Kim, J.S.: Syntheses and conformations of tetrahomodioxaca-
lix[4]arene tetraamides and tetrathioamides. J.Org. Chem. 67,
3165–3168 (2002). doi:10.1021/jo011138i
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