Conformation of N,N′-bis(3-pyridylformyl)piperazine and spontaneous formation of a saturated quadruple stranded metallohelicate

Article abstract of DOI:10.1039/c0dt00337a

Ligand N,N′-bis(3-pyridylformyl)piperazine, L₁, exists in syn and anti conformers in solution state almost in equal proportion. Formation of a saturated quadruple stranded helicate is observed when Pd(NO ₃)₂ is reacted with ligand L₁. In the complexed form the ligand exists in a flattened boat conformation with anti form.

Full text of DOI:10.1039/c0dt00337a

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www.rsc.org/dalton | Dalton Transactions
Conformation of N,N¢-bis(3-pyridylformyl)piperazine and spontaneous
formation of a saturated quadruple stranded metallohelicate†
Himansu Sekhar Sahoo and Dillip Kumar Chand*
Received 20th April 2010, Accepted 17th June 2010
First published as an Advance Article on the web 8th July 2010
DOI: 10.1039/c0dt00337a
Ligand N,N¢-bis(3-pyridylformyl)piperazine, L , exists in
1
syn and anti conformers in solution state almost in equal
proportion. Formation of a saturated quadruple stranded
helicate is observed when Pd(NO
. In the complexed form the ligand exists in a flattened boat
conformation with anti form.
3
2
) is reacted with ligand
L
1
Synthesis of a metallohelicate depends on the intrinsic property
1
of both the metal ion and the chosen ligand. A variety of single-,
2
3
double- and triple -stranded metallohelicates are prepared by
coordination driven self-assembly routes. However, quadruple
stranded metallohelicates with a definite pitch angle are rare
1
in literature and belong to the M
2
L family. The pitch angles
4
5
1
Fig. 2 400 MHz H NMR spectra of L
1 3 2
in (i) CDCl (ii) D O and (iii)
4
reported are 45 degrees and 9 degrees for these structures. Thus
the choice of bidenate ligand plays an important role in producing
such a helicate. Herein, we report a saturated quadruple stranded
metallohelicate and the conformational properties of the chosen
bidentate ligand (Fig. 1).
compound [Pd (L ](NO , 1 in D O.
2
1
)
4
3
)
4
2
ring carbons. This indicates slow conformational change of the
piperazine moiety in L . Such behavior led us to record the proton
NMR of the same sample in different solvents to examine the
1
conformational properties of the compound.
1
The H NMR spectrum of L
1
in D
2
O shows a different
pattern to that of the spectrum in CDCl
3
. The aromatic protons
show multiplets (two different sets of peaks overlapped) and
the methylene protons of the piperazine ring show four signals
consisting of two sharp singlets and two triplet like signals (Fig. 2).
The H–H COSY reveals the protons of the pyridine ring correlated
with each other whereas for the methylene protons, only two triplet
like signals are correlated with each other and the two singlets have
no correlation (see ESI†). This indicates the presence of two sets
of protons corresponding to the piperazine ring as well two sets
1 2 1 4 3 4
Fig. 1 Ligand L and quadruple-stranded helicate [Pd (L ) ](NO ) , 1.
corresponding to the pyridine rings, even though L
1
has a sharp
O shows only
one set of signals for the pyridine ring carbons and four signals
two sets) for the piperazine ring carbons. The presence of two
1
3
melting point. The C NMR of the sample in D
2
The ligand N,N¢-bis(3-pyridylformyl)piperazine, L
1
is prepared
easily by condensing nicotinyl chloride hydrochloride with piper-
1
(
azine. Interpretation of the H NMR spectrum of L
1
recorded in
6
different types of methylene carbon within each set of piperazine
ring is concluded and C–H COSY supports this†.
CDCl
3
is discussed in the literature which is inconsistent with
the structure. Our reinterpretation of the spectrum led to the
understanding of the existence of different conformations of the
ligand in the solution state.
Conformational behavior of compounds with hindered C–N
bond rotation, ring flipping of a six membered rings and nitrogen
inversion in ring systems have been studied by NMR spectroscopy
The proton NMR spectrum of L
1
in CDCl
3
shows two
7
in the literature and N,N¢-dinitrosopiperazine was found to be
almost overlapped broad peaks for the methylene protons of the
1
3
a good comparison for L . N,N¢-Dinitrosopiperazine possess a
1
piperazine ring (Fig. 2). Similarly the C NMR spectrum shows
two broad signals at 47.59 and 42.38 ppm for the piperazine
flattened chair conformation in the solution state and exists in
syn and anti depending on the orientation of oxygen atoms. This
was determined from the ratio of the coupling constants between
Department of Chemistry, Indian Institute of Technology Madras, Chennai,
India, 600036. E-mail: dillip@iitm.ac.in; Fax: +91-44-2257-4202; Tel: +91-
the methylene protons of the piperazine ring. Ligand L was
1
4
4-2257-4224
also thus interpreted to exist in syn and anti conformers in the
†
Electronic supplementary information (ESI) available: experimental
solution state; however, in the solid state only the anti form of
details, NMR, ESI MS, computational study and crystallographic data.
CCDC reference number 745870. For ESI and crystallographic data in
CIF or other electronic format see DOI: 10.1039/c0dt00337a
6
the chair conformation for the piperazine ring is observed. The
1
two singlets in the H NMR at 3.80 and 3.39 ppm correspond to
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the syn form (cis to the carbonyl); the triplet like peaks at 3.65
and 3.55 ppm correspond to the anti form (trans to carbonyl).
The VT NMR spectra† show the peaks for the methylene protons
ligand units in a bridging manner (Fig. 3). Two nitrate anions
are disordered and the other two nitrates are not found. The
flexibility and the different conformations of the ligand allowed
it to reorganize to form such a helicate. A variety of although
not similar but related prismatic structures have been reported in
◦
in piperazine slowly merge and give a broad singlet at 70 C.
The peaks for the pyridine rings were separated and showed four
◦
8
different signals. The coalescence temperature for L
1
is 70 C and
literature.
‡
˚
˚
the energy of activation (DG ) for free rotation of the C–N bond is
The Pd–N distances are 2.010(6) A and 2.013(7) A for Pd-Npy
bonds. The in plane bond angle N–Pd–N are 89.91 and 89.93 . The
Pd–Pd distance in the cage is 9.445(2) A which is slightly longer
than the reported Pd
shows the view of the cage along the Pd–Pd axis (right), which
-
1
◦
ª16.45 kcal mol .
˚
The DFT calculations for the ligand L
1
were undertaken for
˚
L helical compound (8.840(8) A). Fig. 3
4a
both the conformers by using a GAUSSIAN 03 set of algorithms†.
The piperazine ring was frozen as a chair conformation where
upon the energy difference between two forms, syn and anti, was
found to be very small.
2
4
highlights its pseudo D
of the ligands. The helical pitch is approximately 45 which is
the angle subtended by each ligand about the helical axis; thus
4
symmetry and the helical disposition
◦
Reaction of L
provides an off white precipitate within a few minutes which
is found to be a dinuclear compound [Pd (L ](NO , 1. The
proton NMR in D O shows four distinct signals for the pyridine
1
with Pd(NO
3
)
2
in acetonitrile in a 2 : 1 ratio
1a
this represents a saturated quadruply stranded helicate. Another
important feature of this structure is the encapsulation of a nitrate
anion in its cavity, which is not shown in the figure for clarity;
moreover, the anion inside the cavity is disordered. The nitrate is
found at the middle of the Pd–Pd axis. The other nitrate is outside
the cavity and almost at the same distance away from the Pd atom.
Interestingly, the piperazine unit of the ligand in the complexed
form exists as a flattened boat of the trans conformation, which
is reflected in the proton NMR spectrum of the compound being
unlike that of the cis or trans conformations in the free state of
the ligand; thus four distinct signals for the methylene protons
of the piperazine ring are observed for the compound. Hence the
molecule retains its conformation in the solution state.
2
1
)
4
)
3 4
2
ring protons which are downfield shifted when compared with the
free ligand suggesting the symmetric structure for compound 1
(
Fig. 2). The methylene protons of the piperazine ring show four
signals (two doublets and two triplet like signals); each proton
signal correlated to one geminal proton and two vicinal protons,
as confirmed from the H–H COSY spectrum. The C–H COSY
shows one doublet and one triplet like signal attached to a single
carbon atom.†
Thus two sets of diastereotopic protons are present in the
piperazine ring in the complexed form (peaks for ethylene protons
of piperazine ring); suggesting all four protons are in a different
magnetic environment. In the complexed state both the syn and
anti conformers of the ligand are absent as no signals are observed
for them in the proton NMR of 1. Thus the conformation of the
ligand in the complexed form is neither syn nor anti but somewhere
in between, and is a single conformer.
DMSO
rt
cis−Pd
(
en)(NO3)2 + L ⎯⎯⎯→Unidentified products
(1)
1
DMSO
⎡
⎤
(
Unidentified products ⎯⎯⎯→ 1 + Pd en) (NO3)2
⎥
⎦
(2)
ꢀ
⎢
2
6
0
C
⎣
When L
DMSO-d , a mixture of compounds (Fig. 4, eqn (1)) was observed
as indicated by a broad H NMR pattern for the complexes. When
1
and cis-Pd(en)(NO
3
)
2
was mixed in a 1 : 1 ratio in
The ESI mass spectrum shows peaks (and the confirming
isotopic pattern) for fragments containing two palladium atoms
6
1
2
+
◦
1
with different charges. The peak at 761 corresponds to [1 - 2NO
3
]
this solution was heated at 60 C and H NMR spectra were
recorded as a function of time, slow evolution of a new set of
peaks could be observed (Fig. 4, eqn (2)). This new set of peaks
3
+
and 487 corresponds to [1 - 3NO ] .
3
X-ray quality single crystals of 1 were obtained by the slow
evaporation of its solution in water at room temperature. The
molecule crystallizes in the space group P4/n and represents a
helical cage‡. The geometry around each metal is square planner
and the square plane is comprised of four pyridyl nitrogen atoms
of different ligand units; the two Pd(II) units are joined by four
was assigned to compound 1 and the peaks for [Pd(en)
2, were also seen in the H NMR spectra; thus a phenomenon of
2
](NO ) ,
3
2
1
1
Fig. 4 400 MHz H NMR spectra in DMSO-d
6
for (i) ligand L
2x type complexes at room temper-
ature. Spectra showing formation of 1 after heating the solution of
1
; (ii)
Fig. 3 Sphere and stick representation of the crystal structure of
unidentified [{cis-Pd(en)}
x
1 y 3
(L ) ](NO )
2+
[
Pd
2
(L
1
)
4
]
viewed perpendicular to the four fold axis (left) and viewed
along the Pd–Pd axis (right). For clarity, hydrogens and anions are not
shown; each ligand is represented in a different color.
[{cis-Pd(en)}
x
1 y 3
(L ) ](NO )2x for (iii) 6 h ; (iv) 12 h ; (v) 24 h and (vi) 36
◦
h at 60 C.
7
224 | Dalton Trans., 2010, 39, 7223–7225
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9
ligand exchange reactions was observed. For complete conversion
Notes and references
of the unidentified compounds to the discrete compound 1, it took
◦
◦
‡ Crystal data for 1: C64
H
96
N
20
O
48Pd
2
, tetragonal, space group P4/n, a =
3
6 h at 60 C and 1 h at 90 C.†
◦
˚
1
7.0336(7), b = 17.0336(7), c = 17.5784(9)A, a = 90.00, b = 90.00, g = 90.00 ,
V = 5100.3(4) A˚ , Z = 2, T = 293(2) K, r = 1.385 g cm , F(000) = 2192,
3
-
3
When the same reaction was tried in D O by combining ligand
in a 1 : 1 ratio a mixture of compounds
were observed but heating the solution at different temperatures
2
◦
L
1
and cis-Pd(en)(NO
3
)
2
6354 measured reflections (2qmax = 56.70 ), 296 parameters, 0 restraints,
a
b
R (>2s) = 0.0844, Rw = 0.2131.
did not lead to the formation of 1. However, the combination
1 C. Piguet, G. Bernardinelli and G. Hopfgartner, Chem. Rev., 1997, 97,
005and references therein; S. Akine, T. Matsumoto and T. Nabeshima,
Chem. Commun., 2008, 4604; O. Mamula, A. Von Zelewsky and G.
2
of cis-Pd(en)(NO
3
)
2
and L
1
in D
2
O + DMSO-d
6
(400 mL of
D
2
O + 100 mL of DMSO-d
6
) in an NMR tube formed a mixture
Bernardinelli, Angew. Chem., Int. Ed., 1998, 37, 289.
of products and, when the mixture was heated to allow ligand
2
J.-M. Lehn, A. Rigault, J. Siegel, J. Harrowfield, B. Chevrier and D.
Moras, Proc. Natl. Acad. Sci. U. S. A., 1987, 84, 2565; R. Ziessel, A.
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exchange reactions, complete formation of 1 was observed after
◦
◦
2
60 h at 60 C and 1 h at 90 C, thus DMSO facilitates this type of
ligand exchange reaction.† It is quite likely that DMSO stabilizes
the key intermediates in the process by coordination.
In summary, we have studied the conformations of N,N¢-bis(3-
pyridylformyl)piperazine, L , at room temperature which exists in
1
syn and anti forms in different solvents. Spontaneous formation
of a rare variety of quadruple stranded metallohelicate, 1, is
3 T. Riis-Johannessen, G. Bernardinelli, Y. Filinchuk, S. Clifford, N. Dalla
Favera and C. Piguet, Inorg. Chem., 2009, 48, 5512; T. Kreickmann, C.
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2
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Acc. Chem. Res., 1999, 32, 975; G. I. Pascu, A. C. G. Hotze, C. Sanchez-
Cano, B. M. Kariuki and M. J. Hannon, Angew. Chem., Int. Ed., 2007,
demonstrated through self assembly of Pd(NO
3
)
2
1
and ligand L .
Compound 1 encapsulates one nitrate ion at the middle of the
Pd–Pd axis; currently we are studying the possibility of en-
capsulation of other guest molecules or ions inside the helical
cage 1.
4
6, 4374.
4 D. A. McMorran and P. J. Steel, Angew. Chem., Int. Ed., 1998, 37, 3295;
J. Xu and K. N. Raymond, Angew. Chem., Int. Ed., 2006, 45, 6480.
5
6
7
8
M. Fukuda, R. Sekiya and R. Kuroda, Angew. Chem., Int. Ed., 2008,
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4
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This study was supported by DST, India (No. SR/S1/IC-
2
8/2009). We thank Mr V. Ramkumar for collecting the crystal
data and partial solution of the crystal structure. We wish to
acknowledge the help rendered by Dr Sumanta Kumar Padhi,
IMS Okazaki to solve the crystal structure and useful discussions.
We thank Md. Akbar Ali for DFT calculations of one of the
compound. HSS thanks the CSIR, India for a fellowship.
2
009, 28, 4288.
9
D. K. Chand, R. Manivannan, H. S. Sahoo and K. Jeyakumar, Eur. J.
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This journal is © The Royal Society of Chemistry 2010
Dalton Trans., 2010, 39, 7223–7225 | 7225