Synthesis, NMR studies and crystal structure of cryptand 4,7,10,16,21-pentaoxa-1,13-diazabicyclo[11.5.5]tricosane, [H(3.1.1) ·(H2O)3]Cl

Article abstract of DOI:10.1007/s10870-012-0281-1

The cryptand 4,7,10,16,21-pentaoxa-1,13-diazabicyclo[ 11.5.5]tricosane (3.1.1, I) has been synthesized, the crystal structure of the triaquo-hydrochloride salt has been determined by single crystal X-ray crystallography and the ¹H- and ¹³C-NMRchemical shifts have been assigned for the protonated ligand. [(C₁₆H ₃₃N₂O₅)·(H₂O) ₃]Cl, (I), is triclinic with space group P1 and cell constants: a = 9.957(3) A, b = 10.557(5) A, c = 11.324(3) A, α = 95.917(8)°, β = 105.574(8)°, γ = 107.506(9)°, V = 1071.4(3) A³ and Z = 2. In the solid state the cryptand is monoprotonated and holds a water molecule near the central cavity using the hydrogen bonds N13-H13 to O1S, O1S-H1S2 to N1 and O1S-H1S1 to ether oxygen atom O7. Pairs of cryptand molecules are linked by a hydrogen bond network, (O21· · ·H2S2-O2S-H2S1· · ·Cl1) ₂(μ-H3S1-O3S-H3S2)2, that interacts with an ether oxygen (O21, O21A) in each ligand molecule. Springer Science+Business Media, LLC 2012.

Full text of DOI:10.1007/s10870-012-0281-1

J Chem Crystallogr (2012) 42:573–577
DOI 10.1007/s10870-012-0281-1
ORIGINAL PAPER
Synthesis, NMR Studies and Crystal Structure of Cryptand
4,7,10,16,21-Pentaoxa-1,13-diazabicyclo[11.5.5]tricosane,
[
H(3.1.1)ꢀ(H O) ]Cl
2
3
Tam Nguyen
•
Christopher M. Buckley
Gary L. N. Smith
Douglas R. Powell Richard W. Taylor
•
Trevor K. Ellis
•
•
•
Received: 12 August 2011 / Accepted: 17 January 2012 / Published online: 21 February 2012
Ó Springer Science+Business Media, LLC 2012
Abstract The cryptand 4,7,10,16,21-pentaoxa-1,13-diaza-
bicyclo[11.5.5]tricosane (3.1.1, I) has been synthesized, the
crystal structure of the triaquo-hydrochloride salt has been
determined by single crystal X-ray crystallography and the
some heavy metal ions [2]. The original family of crypt-
ands, shown in Fig. 1, consisted of ligands with three
polyethoxy(ethyl) strands joined at nitrogen bridgehead
atoms and were given trivial names indicating the number
of ether oxygen atoms in each bridge (e.g., 2.1.1 has a = 2,
b = c = 1) [3]. All members of the family of cryptands
with a, b, c = 1–3 have been reported [4–7] except for
3.1.1 (I), shown in Scheme 1, although the bicyclic
diamide precursor (V) [8] and analogous compounds with
N-methyl donor atoms instead of oxygen in the 12-mem-
bered ring are known [9, 10]. Cryptand 3.1.1 is a consti-
tutional isomer of 2.2.1 with the same donor atom set
1
13
H- and C-NMR chemical shifts have been assigned for the
protonated ligand. [(C H N O )ꢀ(H O) ]Cl, (I), is triclinic
1
6
33
2
5
2
3
ꢀ
˚
with space group P1 and cell constants: a = 9.957(3) A,
˚
˚
b = 10.557(5) A, c = 11.324(3) A, a = 95.917(8)°, b =
3
˚
1
05.574(8)°, c = 107.506(9)°, V = 1071.4(3) A and
Z = 2. In the solid state the cryptand is monoprotonated and
holds a water molecule near the central cavity using the
hydrogen bonds N13–H13 to O1S, O1S–H1S2 to N1 and
O1S–H1S1 to ether oxygen atom O7. Pairs of cryptand
molecules are linked by a hydrogen bond network, (O21ꢀꢀꢀ
H2S2–O2S–H2S1ꢀꢀꢀCl1) (l-H3S1–O3S–H3S2) , that inter-
(N O ), that differs in the size of the macrocyclic rings that
2 5
comprise each ligand, i.e., 12/18/18 for 3.1.1 compared to
15/15/18 for 2.2.1. Cryptand 3.1.1 should be of interest
because a previous comparison of the constitutional iso-
mers 2.2.2 (18/18/18) and 3.2.1 (21/18/15) showed differ-
ences in the complexation selectivity among alkali- and
alkaline-earth cations (7). The present study reports the
synthesis of the title compound, the X-ray crystal structure
of the monoprotonated hydrate of the hydrochloride salt
2
2
acts with an ether oxygen (O21, O21A) in each ligand
molecule.
Keywords Cryptand ꢀ Crystal structure ꢀ NMR spectra ꢀ
Hydrogen bonds ꢀ Hydrate
1
13
and the assignment of the H- and C-NMR spectra of the
monoprotonated cryptand.
Introduction
Macrobicyclic ligands, or cryptands, have been studied
extensively since their introduction by Lehn and
co-workers [1], in part, because they form stable com-
plexes with alkali- and alkaline-earth cations as well as
Experimental
General Procedures and Materials
All reagents in this study were used as received from
commercial suppliers. Solvents were distilled and stored
T. Nguyen ꢀ C. M. Buckley ꢀ T. K. Ellis ꢀ
G. L. N. Smith ꢀ D. R. Powell ꢀ R. W. Taylor (&)
Department of Chemistry and Biochemistry,
University of Oklahoma, 101 Stevenson Parkway, Norman,
OK 73071-5251, USA
1
13
over molecular sieves. H NMR and C NMR spectra
were obtained at room temperature on a Varian Mercury
VX-300 MHz spectrometer. Assignments were made using
1
13
e-mail: rwtaylor@ou.edu
H and C 1-D experiments and COSY, HSQC and
123

5
74
J Chem Crystallogr (2012) 42:573–577
Fig. 1 Schematic structure of
diazapolyoxa-cryptands
refluxed for 2 h then stirred at room temperature for 36 h.
O
O
O
a
b
c
The flask was cooled in an ice bath, excess BH was quen-
3
ched using water, and the solvent was removed. Then, in the
same flask, 10 mL of 6 N HCl was added and was heated at
N
N
60 °C for 2 h. The acidic solution was removed, water added
and the product was obtained by adjusting the pH to *10
with (C H ) NOH and extraction into CHCl (3 9 100 mL).
2
5 4
3
During the initial stage of solvent removal a white precipitate
formed (0.092 g) that was removed by filtration. Removal of
the remaining solvent gave an oil (0.250 g). The ESI–MS of
the solid and oil fractions of the product showed the same
peaks, 333.2 (M ? H), 355.2 (M ? Na), 167.2 (M ? 2H),
Scheme 1 Structure of
O
O
O
4
,7,10,16,21-pentaoxa-1,13-
diazabicyclo[11.5.5]-tricosane
cryptand 3.1.1, I)
O
N
O
(
1
13
N
and were combined. The H- and C-NMR chemical shifts
and peak assignments for (I) are given in Table 1.
X-Ray Structure Determination of (4,7,10,16,21-Pentaoxa-
1,13-diazabicyclo-[11.5.5]tri-cosane) (I)
HMBC 2-D experiments. Chemical shifts are referenced to
13
the residual proton (d = 7.26 ppm) and C (d = 77.23 ppm)
signals of the solvent, CDCl [11]. ESI mass spectra were
3
Crystals suitable for X-ray crystallography were obtained
recorded using a Micromass Q-Tof instrument in the positive
ion mode.
by adding hexanes to a solution of I dissolved in a minimal
volume of CHCl and placing this solution in a freezer for
3
1
week. The molecular structure and atom-numbering
Synthesis of 4,7,10,16,21-Pentaoxa-1,
1
scheme of the title compound (I) are illustrated in Fig. 2.
Intensity data for this compound were collected using a
diffractometer with a Bruker APEX ccd area detector [12,
3-diazabicyclo[11.5.5]tricosane), Cryptand 3.1.1(I)
The synthesis of I was performed under high-dilution con-
ditions according to the general procedure described by Lehn
et al. [4], as shown in Scheme 2. 4.951 g (25.6 mmol) of II
and 4.251 g (25.7 mmol) of diglycolyl chloride, each dis-
solved in 300 mL of toluene, were added synchronously
from separate dropping funnels to 900 mL of toluene con-
taining 5.795 g (57.3 mmol) of (C H ) N in a 5 L Morton
1
3] and graphite-monochromated Mo Ka radiation
˚
(
k = 0.71073 A). Cell parameters were determined from a
non-linear least-squares fit of 5584 peaks in the range
.26 \ h \ 28.24°. A total of 10996 data were measured in
2
the range 1.91 \ h \ 26.00° using x oscillation frames.
The data were corrected for absorption by the semi-
empirical method [14] and were merged to form a set of
2
5 3
round-bottomed flask over a period of 7 h. The reaction
mixture was filtered, and after *2/3 of the solvent was
removed, the diamide (III) crystallized from solution
4,174 independent data with Rint = 0.0404 and a coverage
ꢀ
of 99.5%. The triclinic space group P1 was determined by
statistical tests and verified by subsequent refinement. The
structure was solved by direct methods and refined by full-
(
4.353 g, 58.6%). 1.38 g (4.75 mmol) of the recovered solid
was dissolved in 55 mL of THF, the solution cooled in an ice
2
matrix least-squares methods on F [15, 16]. The positions
bath, and 1.4 g (36.9 mmol) of LiAlH was added carefully.
4
of hydrogen atoms bonded to carbon were initially deter-
mined by geometry and were refined by a riding model.
Hydrogen atoms bonded to N13 and the water oxygen
atoms (O1S, O2S, O3S) were located by a difference
Fourier synthesis and refined independently. Non-hydrogen
atoms were refined with anisotropic displacement param-
eters. Hydrogen atom displacement parameters were set to
The solution was then heated at reflux for 7 h. The product
(
ESI–MS; m/z = 263, (M ? H) was purified by extraction
from water (pH * 10, Et NOH) into CHCl (3 9 100 mL)
4
3
yielding 1.122 g (90.2%) of cyclic diamine IV. The high-
dilution condensation reaction was repeated using 0.710 g
(
2.71 mmol) of IV and 0.504 g (2.95 mmol) of diglycolyl
chloride, each dissolved in 300 mL of toluene, added syn-
chronously to 400 mL of toluene containing 0.726 g
1.2 times the displacement parameters of the bonded
atoms. Parameters were refined, with restraints on the O–H
2
bond distances for H(1S2) and H(3S2), to give wR(F ) =
(
7.17 mmol) of Et N over a period of 8.0 h. The macrobi-
3
cyclic diamide (V) was purified by column chromatography
on alumina using 5–7% MeOH in CHCl as the eluent to give
2
2
0
.1367 and S = 1.038 for weights of w = 1/[r (F ) ?
3
2
0.0700 P) ? 0.5000 P], where P = [F ? 2F ]/3. The
2
2
(
0
1
.46 g (oil, 47%), ESI–MS, 383.2 (M ? Na). 20 mL of
o c
final R(F) was 0.0576 for the 3349 observed, [F [ 4r(F)],
data. Crystal data and refinement details are presented in
Table 2.
.0 M BH ꢀTHF (20 mmol) was placed in a flask cooled in
3
an ice bath; then 0.40 g (1.11 mmol) of diamide (V), dis-
solved in 25 mL of THF, was added slowly. The mixture was
1
23

J Chem Crystallogr (2012) 42:573–577
575
Scheme 2 Synthesis of
cryptand 3.1.1 (I)
O
O
O
O
O
O
O
Cl
O
Cl
O
Cl
O
Cl
O
LiAlH4
O
O
O
O
O
BH •THF
3
O
N
O
NH2
H2N
toluene,
Et N
Et4NOH
toluene,
HCl,
NH
HN
N
3
Et N
Et NOH
3
4
X
X
X
X
II
III (X = O)
IV (X = 2H)
V (X = O)
I (X = 2H)
1
13
Table 1 H- and C-NMR chemical shifts d(ppm) and results of COSY, HSQC and HMBC experiments
a
1
b
13
C
H d(ppm)
COSY (H–H)
C d(ppm)
HSQC (C–H)
HMBC (C(-)
n
H)
2
3
5
6
1
1
1
(12)
3.20 4H, t
3.20–3.86
61.6
66.8
69.8
70.4
57.4
66.3
66.3
61.6–3.20
66.8–3.86
69.8–3.62
70.4–3.62
57.4–3.30
66.3–3.78
66.3–4.02
61.6–3.30
(11)
3.86 4H, m
3.62 4H, s
3.62 4H, s
3.30 8H, m
3.78 4H, dt
4.02 4H, m
–
66.8–3.20,3.62
69.8–3.62
70.4-3.62
57.4–3.20,4.02
66.3–3.30
‘‘ ‘‘
(9)
–
(8)
–
4(18,19,23)
5(17,20,22)
5(17,20,22)
3.30–3.78,4.04
3.78–4.02
–
s singlet, t triplet, dt doublet of triplets, m multiplet
a
Carbon number from Fig. 2
b
Chemical shift, number of equivalent protons, resonance multiplicity
Results and Discussion
constants, at pH * 10 most of the cryptand is likely to be
? -
present as [H(3.1.1) ], Cl during the extraction step.
1
3
The synthesis followed existing literature procedures;
however, the isolation of the monohydrochloride product
probably resulted from incomplete neutralization of
The C-NMR spectra in CDCl showed only six peaks,
3
which is consistent with the approximate C2v symmetry
expected for 3.1.1 in solution. The proton spectrum also
has the appropriate number of peaks, but is complicated is
2
?
H (3.1.1) that was formed during the hydrolysis of the
2
bis-borane adduct with aqueous HCl. The first protonation
constant for the related cryptand, 2.1.1, is between 10.64
and 11.32 [17]. Therefore, if I has similar protonation
several ways. Considering the chemical shifts, d3.1.1,ave
3.2 for NCH , which is significantly downfield compared
=
5
2
to dave * 2.7 for the analogous protons in 2.1.1, 2.2.1,
2
.2.2 and 3.2.2 [4]. Likewise, for NCH CH O d
=
3.1.1,ave
2
2
3
.8 compared to *3.6 for the analogous protons in other
9
cryptands. In the case of the singlet for OCH CH O,
2
2
d3.1.1 = 3.6 is close to the value of *3.7 for the other
2
cryptands [4]. The downfield shifts for 3.1.1 decrease as the
protons become further removed from the nitrogen atom.
However, if one compares the d3.1.1 values (3.2 , 3.8 , 3.6 )
5
9
2
to the corresponding values of dave (3.1 , 3.8 , 3.5 ) for the
7
8
9
bis(N-BH ) adducts of cryptands 2.1.1, 2.2.1, 2.2.2 and
3
3.2.2 [4] the downfield shifts compared with 3.1.1 almost
disappear. In view of the electron withdrawing properties
of the BH groups for the adjacent nitrogen [18], the values
3
and pattern of d3.1.1 values are consistent with the presence
of a proton on one of the nitrogen atoms. The splitting
multiplicities in 3.1.1 are also of interest. In the longer
bridge the singlet (OCH CH O) and pair of triplets
2
2
(NCH CH O) are the same as found for the other cryptands
2 2
and the corresponding bis-NꢀBH adducts [4], indicating
3
that axial-equatorial interconversion for these ethylene
linkages is fast on the NMR time scale. However, the
Fig. 2 Atom labeling scheme for 3.1.1. Displacement ellipsoids are
shown at the 50% probability level
123

5
76
J Chem Crystallogr (2012) 42:573–577
˚
Table 2 Crystal data and structure refinement for cryptand 3.1.1 (I)
Table 3 Hydrogen bond lengths (A) and angles (°) for (I)
CCDC deposit no.
Color/shape
832360
D–HꢀꢀꢀA
d(D–H)
d(HꢀꢀꢀA)
d(DꢀꢀꢀA) \(DHA)
Colorless plate,
0
N(13)–H(13)ꢀꢀꢀO(1S)
O(1S)–H(1S1)ꢀꢀꢀO(7)
O(1S)–H(1S1)ꢀꢀꢀO(4)
O(1S)–H(1S2)ꢀꢀꢀN(1)
O(2S)–H(2S1)ꢀꢀꢀCl(1)
O(2S)–H(2S2)ꢀꢀꢀO(21)
O(3S)–H(3S1)ꢀꢀꢀCl(1)
0.91(3)
0.83(3)
0.83(3)
1.84(3)
2.19(3)
2.55(3)
2.750(3) 171(3)
3.016(3) 169(3)
3.041(2) 119(2)
.40 9 0.18 9 0.03 mm,
Empirical formula
Formula weight
16
C H
39ClN
2 8
O
422.94
100(2)
0.851(10) 2.180(11) 3.027(3) 174(3)
Temperature (K)
1.00(3)
0.93(3)
0.83(3)
2.18(3)
2.05(3)
2.37(3)
3.174(2) 171(3)
2.906(3) 153(3)
3.202(2) 175(3)
Crystal system, space group
Unit cell dimensions
Triclinic, Pꢀ1
˚
a (A)
9.957(3)
O(3S)–
H(3S2)ꢀꢀꢀCl(1)#1
0.855(10) 2.352(11) 3.200(2) 172(3)
˚
b (A)
10.557(3)
11.324(3)
95.917(8)
105.574(8)
107.506(9)
1071.4(5)
2, 1.311
˚
c (A)
Symmetry transformations used to generate equivalent atoms:
1 -x ? 2, -y, -z ? 2
a (°)
b (°)
c (°)
#
with O4, with an O1S–H1S1ꢀꢀꢀO4 angle of 119(2)°.
Although structures of a number of protonated cryptands
are known, only a few of these involve the monoprotonated
ligands [19, 20]. In each case a water molecule is held in an
3
˚
Volume (A )
3
Z, density, calculated (g/cm )
-
1
)
Absorption coefficient (mm
0.221
h range for data collection,
deg
1.91–26.00
18-membered macrocyclic ring of the ligand cavity by
three H-bonds involving alternating heteroatoms; one with
N–H and two from H(water) to ether O, similar to the
situation found with I. One 18-membered ring of 3.1.1
forms an approximate plane defined by heteroatoms
Data measured
10996
Independent/observed data
4174 [Rint = 0.0404]/3349
I [ 2r(I)]
[
Data/restraints/parameters
2
Goodness-of-fit on F
4174/2/265
1.038
˚
N1,O4,O7,O10,N13,O21 (mean dev. = 0.2837 A). This
plane has a dihedral angle of 90.2°(3) with the plane
defined by N1, O16, and N13 of the other bridging seg-
ment. The torsion angle sequence for the X–C–C–Y seg-
ments (X, Y = O, N) around this 18-membered ring is
wR2 (all data)
0.1367
R1(observed data)
0.0576
Largest diff. peak and hole
(
0.538 and -0.230
3
e/A )
˚
(
aga) , where g and a indicate gauche and antiperiplanar
6
2
o
2
c
2
2
o
2
1=2
wR2 ¼ fR½wðF ꢁ F Þ ꢂ=R½wðF Þ ꢂg
torsion angles, respectively [21, 22]. This conformation has
alternating heteroatoms on opposite sides of the heteroatom
plane (i.e., N1,N13,O7 and O4,O10,O21). This conforma-
tion, with approximate D3d symmetry, is also found for
18-membered crown and diaza-crown ether complexes
with several metal ions [23]. The similar symmetry of the
planar 18-membered ring in 3.1.1 provides alternating
heteroatoms (NH, N, O) suitably placed for H-bond inter-
actions with water and complementarity of H-bond sites
R1 ¼ RkFojꢁjFck=RjFoj
increased splitting multiplicity for the NCH CH O seg-
2
2
ments in the 12-membered ring shows that these confor-
mational changes are restricted, at least at room
temperature. These findings are consistent with those
expected for a protonated, possibly hydrated, form of 3.1.1.
The structure of I, shown in Fig. 2, reveals that the
ligand crystallizes as the tris-aquo-monohydrochoride
complex. One water molecule is present near the center of
the 18-membered ring defined by the heteroatoms
N1,O4,O7,O10,N13 and O21 on the side of the ring
opposite to the short bridging segment containing O16. The
?
between the monoprotonated cryptand, H(3.1.1) , and
water. Two molecules of 3.1.1 are linked together via an
-
H-bond network utilizing O21ꢀꢀꢀH(OS2)HꢀꢀꢀCl ꢀꢀꢀH(OS3)H
-
subunits, as shown in Fig. 3. A similar (Cl ) (HOH)
2
4
2
?
bridged network has been found with H (2.1.1) [24];
2
however, in that case there was no interaction of the net-
work with the cryptand O or N atoms.
˚
oxygen atom of the water is 0.720(4) A distant from this
plane and is held in place by three strong hydrogen bonds
(
see Table 3) involving N1, N13 and O7. The proton of
Supporting Information Available
N13 (H13) forms a hydrogen bond to the oxygen of the
water molecule while one of the hydrogen atoms on water
X-ray crystallographic files, in CIF format, for the structure
determination of (I) (CCDC 832360) have been deposited
with the Cambridge Crystallographic Data Center, CCDC:
26091. Copies of this information may be obtained free of
(
H1S2) forms an H-bond with N1. The other hydrogen on
water (H1S1) forms a strong hydrogen bond to ether oxy-
gen O7. In addition, H1S1, forms a weak hydrogen bond
1
23

J Chem Crystallogr (2012) 42:573–577
577
?
-
2
Fig. 3 Hydrogen bond network for H(3.1.1) with H O and Cl
charge from the Director, CCDC, 12 Union Road, Cam-
bridge, CB2 1EZ (fax: ?44-1223-336033; email: depos-
it@ccdc.cam.uk or at www: http://www.ccdc.cam.ac.uk).
10. Bazzicalupi C, Bencini A, Bianchi A, Fusi V, Giorgi C, Paoletti
P, Valtancoli B (1994) J Chem Soc Dalton Trans 3581. doi:
1
0.1039/DT9940003581
1
1. Fulmer GR, Miller AJM, Sherden NH, Gottlieb HE, Nudelman A,
Stoltz BM, Bercaw JE, Goldberg KI (2010) Organometallics
29:2176. doi:10.1021/om100106e
Acknowledgments This study was supported by the Oklahoma
Center for the Advancement of Science and Technology (grant HR06-
12. Data collection: SMART Software Reference Manual (1998)
Bruker AXS Inc., Madison
13. Data reduction: SAINT Software Reference Manual Bruker
(1998) Bruker AXS Inc., Madison
1
0
13). The authors also thank the National Science Foundation (CHE-
130835) and the University of Oklahoma for funds to acquire the
diffractometer and computers used in this study.
1
1
1
1
1
1
2
4. Sheldrick GM (2002) SADABS. University of Gottingen,
Germany
5. Sheldrick GM (2008) Acta Cryst A64:112–122. doi:10.1107/
S0108767307043930
6. Sheldrick (1995) International tables for crystallography, Vol C,
Tables 6.1.1.4, 4.2.6.8 and 4.2.4.2. Kluwer, Boston
7. Izatt RM, Bradshaw JS, Nielsen SA, Lamb JD, Christensen JJ,
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