Solid-state structures and solution analyses of a phenylpropylpyridine N-oxide and an N-methyl phenylpropylpyridine

Article abstract of DOI:10.1002/asia.200800255

The crystal structures of phenylpropylpyridine-N-oxide and N-methyl-phenylpropylpyridinium iodide are compared, revealing that hydrogen bonding with the solvent molecule plays an important role in the N-oxide compound, whilst electrostatic interactions ar

Full text of DOI:10.1002/asia.200800255

FULL PAPERS
DOI: 10.1002/asia.200800255
Solid-State Structures and Solution Analyses of a Phenylpropylpyridine N-
Oxide and an N-Methyl Phenylpropylpyridine
Isabella Richter,[a] Mark R. Warren,[a] Jusaku Minari,[b] Souad A. Elfeky,[a] Wenbo Chen,[a]
Mary F. Mahon,[a] Paul R. Raithby,*[a] Tony D. James,[a] Kazuo Sakurai,[b] Simon J. Teat,[c]
Steven D. Bull,[a] and John S. Fossey*[a]
Abstract: The crystal structures of phe-
nylpropylpyridine-N-oxide and N-
the solid-state orientation of the N-me-
thylated compound. Fluorescence spec-
troscopy and NOESY indicate that in
contrast to the previously reported pyr-
idinium iodide, the N-oxide is not sub-
ject to intramolecular p-stacking, as
judged by excimer emission and a lack
of corresponding cross peaks, respec-
tively.
methyl-phenylpropylpyridinium iodide
are compared, revealing that hydrogen
bonding with the solvent molecule
plays an important role in the N-oxide
compound, whilst electrostatic interac-
tions are predominant in controlling
Keywords: cations · fluorescence ·
hydrogen bonds · alkylpyridines · p-
stacking
Introduction
strating that aromatic–aromatic interactions are solely re-
sponsible for conformational control is well known.[16,17] In
contrast to more conformationally biased systems that have
been exploited for asymmetric synthesis and control supra-
molecular architecture,[18–21] we recently demonstrated that
subtle intramolecular cation–p interactions of flexibly
linked, conformationally mobile pyridinium species (e.g.,
compound 1 in Figure 1) could be detected using fluores-
cence spectroscopy.[22,23]
Aromatic–aromatic interactions are often required for a
high degree of control in asymmetric synthesis,[1–4] and p-
stacking interactions have been implicated in a number of
template directed syntheses.[5–7] Stacking interactions are
also proposed to be vital in many biological recognition sce-
narios.[8–12] Model systems have been developed to probe
these interactions;[13–15] however the difficulty for demon-
[a] I. Richter, M. R. Warren, S. A. Elfeky, W. Chen, M. F. Mahon,
Prof. P. R. Raithby, T. D. James, S. D. Bull, Dr. J. S. Fossey+
Department of Chemistry
The University of Bath
Claverton Down, Bath, BA2 7AY (UK)
Fax : (+44)1225386231
E-mail: j.s.fossey@bham.ac.uk
p.r.raithby@bath.ac.uk
[b] J. Minari, K. Sakurai
Figure 1. Phenylalkylpyridine derivatives 1 and 2.
Current Address: Faculty of Environmental Engineering
Department of Chemical Process and Environments
The University of Kitakyushu, 1-1, Hibikino, Wakamatsu-ku
Kitakyushu, Fukuoka, (Japan)
Whilst our interest in N-alkylpyridinium structures (1)
stems from a desire to understand the conformation of cata-
lytic species and their implications for (stereo)selectivity, we
wished to probe the solid-state properties of cation–p motifs
to enable comparison of solution and solid-state data. Avas-
thi et al. have shown that propylene linked pyrazolo [3,4-
d]pyrimidines favor folded conformations in the solid
state.[24,25] We had previously reported strong evidence for
p-stacking of the cationic compound 1 in solution, hence we
[c] S. J. Teat
Advanced Light Source
Lawrence Berkeley National Laboratory
Berkeley, CA 94720 (USA)
[+] New Address: School of Chemistry
University of Birmingham
Edgbaston, Birmingham, B15 2TT (UK)
Supporting information for this article is available on the WWW
under http://dx.doi.org/10.1002/asia.200800255.
194
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Chem. Asian J. 2009, 4, 194 – 198

anticipated that this structure might also display p-stacking
in the solid state, and therefore decided to probe its solid-
state structure/orientation. Consequently, we now report the
solid-state structure of N-methyl-pyridinium salt 1 and the
closely related neutral phenylalkylpyridine N-oxide deriva-
tive 2.
Compound 1 crystallises in the orthorhombic space group
Pnma with Z=12, that is, with three structurally similar, in-
dependent half molecules in the crystallographic asymmetric
unit. Each cation sits on a crystallographic mirror plane,
which generates the other half of the molecule. However,
there are subtle differences between the three molecules. In
two of the three cations, namely, cation (a) (C(1)–C(13))
and cation (b) (C(14)–C(26)), the phenyl rings C(1)–C(6)
and C(14)–C(19), respectively, lie in the crystallographic
mirror planes, while the corresponding pyridine rings (N(1),
C(10)–C(12)) and (N(2), C(23)–C(25)) are bisected by the
crystallographic mirror plane. This means that the dihedral
angle between the phenyl and pyridine ring in each mole-
cule is precisely 908 by crystallographic symmetry. However,
in the third molecule, cation (c) (C(27)–C(37)) both the
phenyl ring (C(27)–C(30)) and the pyridine ring (N(3),
C(34)–C(36)) are bisected by crystallographic mirror planes
so that these planes are not required to be perpendicular by
crystal symmetry and the dihedral angle between the planes
of these two rings is 62.58. The torsion angles along the ali-
phatic chains in the three molecules are all 1808 by crystal
symmetry. The three half iodine anions also sit on crystallo-
graphic mirrors. The bond parameters within the cations lie
within the normal ranges.
Results and Discussion
Single Crystal X-Ray Diffraction
Though compound 1 was a little sensitive to light in solu-
tion, small plate-like crystals were obtained and found to be
stable in ambient conditions. These crystals of 1 were suita-
ble for diffraction analysis utilising the diffraction facilities
on Beamline 11.3.1 at the ALS, Lawrence Berkeley National
Laboratory, and its molecular and crystal structures are illus-
trated in Figures 2 and 3, respectively.
The crystal packing (Figure 3) shows that electrostatic
cation–anion interactions dominate in the molecule. The
anions lie in the channels parallel to the crystallographic c
axis with the polar (C5H4NACTHNUTRGNE(UNG CH3)) groups pointing towards
these anion channels. The cations are arranged so that adja-
cent groups have their polar end groups pointing in opposite
directions. There is little indication of either hydrogen bond-
ing or of CH–p interactions between the cations.[26]
To allow comparison between different functionality, crys-
tallisation of a number of structural variations was attempt-
ed. Despite failing to obtain suitable crystals from related
cationic alkyl and benzyl halide and triflate salts, we were
delighted to obtain crystals of the aquated compound 2 suit-
able for X-ray diffraction analysis, the molecular and crystal
structure of which is shown in Figures 4 and 5.
+
À
À
The aquated compound [(C6H5)ACHTUNRGTNE(GNU CH2)3(C5H4N O )]H2O
2 crystallises in the orthorhombic space group Pcab (non-
standard setting of Pbca, No. 61) with Z=8. The bond pa-
rameters in the unique molecule lie within the expected
ranges and the dihedral angle between the phenyl ring
(C(9)–C(14)) and the pyridine ring (N(1), C(1)–C(5)) is
only 4.38, so that within the molecule in the solid state,
these rings are almost parallel but the distance between the
centroids of the two rings, at 6.08 ꢁ, excludes the possibility
of intramolecular p–p-stacking. The observed dihedral angle
is comparable to the crystallographically constrained angles
(CH3))]+IÀ
Figure 2. The crystal structure of [(C6H5)ACHTUNGTREN(NUNG CH2)3ACHTUNGTREG(NNNU C5H4NACHNUTGTRENNUGN 1
showing the three units with atomic numbering scheme. The two halves
of the pyridine ring (N(1), C(10)–C(12)) are related by the symmetry op-
eration x, 1.5Ày, z, and all the other halves of the rings by the symmetry
operation x, 0.5Ày, z.
Abstract in Japanese:
À
À
À
of 62.58 and 90.08 in 1. The torsion angles C(9) C(8) C(7)
À
À
À
C(6) and C(3) C(6) C(7) C(8) are 67.28 and 70.38, respec-
tively.
The intermolecular interactions are dominated by the hy-
drogen bonding network between the solvent water mole-
cule and the oxygen atom of the N-oxide compound.
Strands of hydrogen bonds run along the a axis through the
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195

P. R. Raithby, J. S. Fossey et al.
FULL PAPERS
crystal (Figure 5) and the pa-
À
rameters
H(2B)···O1
for
the
and
O(2)
À
O(2)
H(2A)···O(1) hydrogen bonds
are
H(2B)···O(1),
2.01 ꢁ,
À
O(2)···O(1),
H(2B)···O(1),
H(2A)···O(1),
O(2)···O(1),
2.91 ꢁ,
173.98,
O(2)
and
2.01 ꢁ,
À
O(2)
2.89 ꢁ,
H(2A)···O(1), 165.38, respec-
tively, where the two O(1)
atoms are related to the
O(2) atom by the symmetry
operations x, y, z and 0.5+x,
1.5Ày, z.[27]
Spectroscopy
We previously reported that
NOE provided us with qualita-
tive information on intramolec-
ular interactions in 1 and relat-
ed structures.[22] Under compa-
rable conditions, we could not
confidently ascribe a stacking
nature between the pyridyl N-
Figure 3. Crystal packing of 1 showing the channels of IÀ ions running parallel to the c axis.
Figure 5. The crystal packing of 2.H2O showing hydrogen bonding along
the a axis.
oxide and phenyl rings based on the NOESY spectrum of 2,
which suggests that intramolecular interactions in the cation
of 1 are not equivalent to those of the overall neutral unim-
olecular N-oxide 2.
Consequently we utilised fluorescence spectroscopy as a
tool for the analysis of p–p interactions in solution, that is,
excimer emission as evidence for p-stacking as depicted in
the stacked representation in Figure 1.
A pre-scan of 2 (conc=1ꢂ10À4 m in CH2Cl2) suggested an
excitation wavelength of 315 nm leading to an emission at
ꢀ380 nm should be used. If this observed emission were a
Figure 4. Crystal structure of one unit of [(C6H5)ACHTNUTGRNEUNG
(CH2)3(C5H4N+-
OÀ)]H2O 2. Anisotropic displacement parameters have been drawn at
the 50% probability level and atom numbering scheme is also shown.
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Chem. Asian J. 2009, 4, 194 – 198

Solid-State Structures and Solution Analyses of Phenylpropylpyridines
result of p-stacking (excimer emission), a corresponding
shorter wavelength peak should be observed in N-oxide 4
which would not be subject to the same kind of intramolecu-
lar p-stacking. To bench mark the fluorescence spectroscopy
results, spectra of N-methyl phenylpropylpyridinium iodide
1, N-methyl phenylpropylpyridine 3, and pyridine N-methyl
pyridinium iodide 5 were recorded under the same condi-
tions and the results are presented in Figure 6. Under these
Conclusions
Through the analysis of the solid-state structures of [(C6H5)
CATHNUGTERNN(UNG CH2)3ACTHGNUNERT(NGNU C5H4NAHCTUNERTGNNNUG 1 and [(C6H5)AHCTNUGTREG(NNNU CH2)3(C5H4N
(CH3))]+IÀ
+
À
OÀ)]H2O 2, it is apparent that different intermolecular inter-
actions dominate in the two cases. In 1, electrostatic interac-
(CH3))]+ cations
tions between the [(C6H5)CAHTGNUTRNEN(UNG CH2)3AHCUTNRTGEG(NNNU C5H4NACHTUNGTRENNGUN
and the IÀ ions represents the major packing interaction.
In the crystal structure of 2, the presence of water is of
considerable importance. The major crystal structure-deter-
mining feature is the hydrogen bonding network formed be-
tween the water molecule and the N-oxide oxygen atom. Hu
et al.[28] and others have also implicated hydrogen bonding
as the key factor for the characteristic T-shaped interactions
and p-stacking in conformationally rigid systems.[29,30] There
is also evidence for the presence of weak CH–p interactions
between the phenyl and pyridine rings on adjacent mole-
cules. Despite the presence of aromatic rings, there is no evi-
dence of graphitic-like p–p-stacking interactions. This inter-
action may be precluded by weak electrostatic repulsions
from the OdÀ N-oxide oxygen atom.
The solid-state structures of 1 and 2.H2O are dominated
by electrostatic and hydrogen bonding channel-like architec-
tures, respectively, which results in molecular conformations
that do not display the archetypal intermolecular p-stacking
interactions previously revealed in the solution state of 1 by
fluorescence spectroscopy.[22] Hence, the solution and solid-
state structures must be very different. It remains unclear
what the effect on the solid-state structure would be if water
was removed from 2.
In solution, NOESY failed to provide evidence of N-
oxide p-stacking along with a reduction in relative fluores-
cence between phenyl containing 2 versus pyridine N-oxide
5. It may be concluded that a system which is ideally suited,
on steric grounds, to possess intramolecular p-stacking ap-
pears not to offer any evidence for its presence. Although
another kind of inter- or intra- molecular interaction may be
operating that could explain the relative reduction in fluo-
rescence, conformationally flexible phenyl-linked N-oxides
appear unsuitable as p-stacking building blocks for solid-
state materials.
Figure 6. a) Compounds compared by Fluorescence Spectroscopy.
b) Emission spectra of compounds 1--5, 1ꢂ10À4 m (CH2Cl2), excitation at
315 nm.
Experimental Section
conditions, 1, 3 and 5 elicit the same kind of response as we
already reported under different conditions, namely, excimer
emission from 1 (ꢀ400 nm), accompanied by an absence of
emission from 3 and 5 at the same wavelength. However,
pyridine N-oxide 4 has a relatively intense fluorescence in
the same region, which is accompanied with a less intense
peak from phenylpropylpyridine N-oxide 2 in the same
region of the spectrum, and as such, no excimer peaks were
detected.
Synthesis
1: 4-(3-Phenylpropyl)pyridine methyl iodide. As previously reported.[22]
2: 4-(3-Phenylpropyl)pyridine N-oxide.[31–33] 4-(3-Phenylpropyl)pyridine
(1.0 g, 5 mmol) was dissolved in acetonitrile/water (2 mL:8 mL) and
heated to 758C. Hydrogen peroxide (3 mL (35%), 0.1 mmol) was added
dropwise with stirring. After 72 h the mixture was evaporated to dryness
and the residue purified by flash chromatography (silica gel, ethyl ace-
1
tate/methanol=50:50 ) to afford 2. H NMR (500 MHz; CDCl3): d=1.97
(quin, J=7.7 Hz, 2H, CH2), 2.65 (m, 4H, 2xCH2), 7.08 (d, J=6.6 Hz, 2H,
Py CH), 7.16 (d, J=7.9 Hz, 2H, PhCH), 7.21 (t, J=7.3 Hz, 1H, Ph CH),
7.30 (m, 2H, Ph CH), 8.12 ppm (d, J=6.7 Hz, 2H, NCH); 13C{1H} NMR
(75 MHz; CDCl3): d=142.28, 141.52, 139.22, 128.91, 128.76, 126.55,
126.38, 35.47, 34.10, 32.01 ppm; m.p.=60–618C; Acc. mass: Bruker, Dal-
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P. R. Raithby, J. S. Fossey et al.
FULL PAPERS
tonics, MICROTOF(ESI, positive): m/z (%) calcd for C14H15NO:
214.1231 [M+H]+; found: 214.1227.
tian Government (SAE fellowship), the EPSRC (PRR Senior Research
Fellowship, PA and MRW studentships), and the Leverhulme Trust (JSF
and WC F/00351/P).
X-Ray Crystallography
Data collection and reduction: A suitable single crystal of 1 was glued
onto the end of a glass fibre while a crystal of 2 in inert oil was mounted
on a glass fibre. Data were measured on a Bruker AXS APEXII CCD
diffractometer on Station 11.3.1 at the ALS, Lawrence Berkeley National
Laboratory (1) using silicon monochromated radiation of wavelength l=
0.7749 ꢁ or using Mo-Ka radiation (l=0.71069 ꢁ) with a Bruker Nonius
Kappa CCD diffractometer at the University of Bath (2) and both instru-
ments were fitted with an Oxford Cryostream low-temperature attach-
ment although the data for 1 was collected at room temperature because
the crystal underwent a destructive phase change at lower temperatures.
Structure solution and refinement: Structures were solved by direct meth-
ods (SHELXS-86)[34] and subjected to full-matrix least-squares refine-
ment on F2 (program SHELXL-97).[35] For both structures all the non-hy-
drogen atoms were refined with anisotropic displacement parameters. In
the structure of 1, all the hydrogen atoms were placed in idealised posi-
tions and allowed to ride on the relevant carbon atom with the isotropic
displacement parameter refined as 1.2 times that of the attached carbon
atom for the methylene and aromatic hydrogen atoms and 1.5 times for
the methyl hydrogen atoms. In each cation, the methyl group attached to
the pyridine ring was disordered across a mirror plane and so each hydro-
gen was refined over two positions with an occupancy of 0.25. The same
parameters were used to refine the hydrogen atoms in 2 except for the
hydrogen atoms attached to the oxygen of the water molecule. The water
hydrogen atoms were located in the electron density difference map, and
their positions were DFIXed at 0.9 ꢁ from the oxygen atom and they
were each assigned an independent isotropic displacement parameter.
Refinement continued until convergence was reached. A weighting
scheme which gave a relatively flat analysis of variance was introduced in
the final cycles of refinement. The final electron density difference map
for each structure showed no significant regions of residual electron den-
sity.
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Crystal data for 1: C15H18IN, M=399.20, crystal dimensions: 0.20ꢂ0.10ꢂ
0.01 mm, orthorhombic, space group Pnma, T=288 K, a=32.183(7), b=
8.1961(17), c=17.375(4) ꢁ, V=4583.3(16) ꢁ3, Z=12, 1cald =1.475 gcmÀ3
,
m=2.586 cmÀ1
, 2.76<q<25.508, 17483 reflections measured, RACHTNGUTREN(NUGN int)=
0.045, 3496 unique reflections, 2705 observed reflections (I>2s(I)), R1=
0.036 for observed data and wR2=0.101 for all data.
Crystal data for 2: C14H17NO2, M=231.29, crystal dimensions: 0.50ꢂ
0.30ꢂ0.30 mm, orthorhombic, space group Pcab, T=150 K, a=9.3420(1),
b=11.7920(2), c=21.8200(4) ꢁ, V=2403.71(7) ꢁ3, Z=8, 1cald
=
ACHTUNGTRENNUNG
1.278 gcmÀ3, m(Mo-Ka)=0.085 cmÀ1, 3.74<q<27.468, 33661 refleed data
and wR2=0.0983 for all data.
Fluorescence Spectroscopy
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Acknowledgements
The Advanced Light Source is acknowledged for granting beamtime
which is supported by the Director, Office of Science, Office of Basic
Energy Sciences, of the U.S. Department of Energy under Contract No.
DE-AC02-05CH11231. Dr. J. P. Lowe and Dr. A. T. Lubben are thanked
for assistance with NMR spectroscopy and mass spectrometry, respective-
ly. We are grateful to the DAAD (IR scholarship), the Royal Society
(JM, KS, SDB Joint Project and JSF Research Grant 2007/R2), the Egyp-
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Received: July 4, 2008
Published online: October 27, 2008
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Chem. Asian J. 2009, 4, 194 – 198