Synthesis and structural characterization of 1-[2-(5-Nitro-1H-indol-2-yl) phenyl]methylpyridinium chloride

Article abstract of DOI:10.3390/molecules16097627

In the course of studies on hybrid antibacterials incorporating 2-aryl-5-nitro-1Hindole moieties as potential bacterial NorA efflux pump inhibitors, the compound 1-[2-(5-nitro-1H-indol-2-yl)phenyl]methylpyridinium chloride (2) was synthesized and structur

Full text of DOI:10.3390/molecules16097627

Molecules 2011, 16, 7627-7633; doi:10.3390/molecules16097627
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molecules
ISSN 1420-3049
www.mdpi.com/journal/molecules
Communication
Synthesis and Structural Characterization of 1-[2-(5-Nitro-1H-indol-2-
yl)phenyl]methylpyridinium Chloride
John B. Bremner 1,*, Siritron Samosorn 2, Brian W. Skelton 3 and Allan H. White 3
1
School of Chemistry, University of Wollongong, Wollongong, NSW 2522, Australia
2
Department of Chemistry, Srinakharinwirot University, Bangkok 10110, Thailand
3
School of Biomedical, Biomolecular and Chemical Sciences, Chemistry M313,
The University of Western Australia, Crawley, W.A. 6009, Australia
* Author to whom correspondence should be addressed; E-Mail: john_bremner@uow.edu.au;
Tel.: +612-42214255; Fax: +612-42214287.
Received: 29 July 2011; in revised form: 22 August 2011 / Accepted: 25 August 2011 /
Published: 6 September 2011
Abstract: In the course of studies on hybrid antibacterials incorporating 2-aryl-5-nitro-1H-
indole moieties as potential bacterial NorA efflux pump inhibitors, the compound 1-[2-(5-
nitro-1H-indol-2-yl)phenyl]methylpyridinium chloride (2) was synthesized and structurally
characterized. This pyridinium chloride salt crystallized in the monoclinic space group
P21/c with the following unit cell dimensions: a 10.274(3) Å, b 13.101(4) Å, c 13.439(4)
Å, β 107.702(7)°, V 1723.2(9) Å3, Z (f.u.) = 4; R1 = 0.048, and wR2 = 0.13. Of interest in
the single crystal X-ray structure is the (intramolecular) disposition of the pyridinium plane
over the indole heterocyclic residue [interplanar dihedral angle 17.91(4)°].
Keywords: indole; pyridinium salt; X-ray crystal structure
1. Introduction
Quaternary pyridinium salts are of continuing interest as biocidal agents [1-4] and we have
synthesised one such salt as part of a broader project on new hybrid antibacterial agents incorporating
2-aryl-5-nitro-1H-indole moieties as bacterial NorA efflux pump inhibitors [5-9]. This pump in the
human bacterial pathogen, Staphylococcus aureus, is known to compromise the activity of a range of
antibacterials including biocidal quaternary salts and the quaternary alkaloid salt berberine [10]. In an
attempt to introduce an N-tosyl protecting group into the nitro indolic pump inhibitor 1 [5], reaction

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Molecules 2011, 16
with p-toluenesulfonyl chloride in the presence of pyridine as a base was investigated. This resulted,
however, in the novel substituted pyridinium chloride salt 2, which was a potential hybrid antibacterial
with an antibacterial benzylic pyridinium group (and potential NorA pump substrate) tethered to a
NorA efflux pump blocking component. The synthesis and characterization of 2, together with a single
crystal X-ray structure determination, is now reported in this paper.
2. Results and Discussion
The pyridinium salt 2 was synthesised from the previously described [5] indole alcohol 1 upon
reaction with p-toluenesulfonyl chloride in the presence of pyridine followed by work up of the
reaction mixture with exposure to hydrochloric acid (Scheme 1). The salt 2 was isolated in moderate
yield and was characterized through spectroscopic data. The absence of any evidence for the presence
1
of an aromatic methyl group (for the p-toluenesulfonyl functionality) was clear from the H- and
13C-NMR data, while the incorporation of a pyridinium moiety was indicated from the characteristic
low field signals in the aromatic region of the 1H- and 13C-NMR spectra. Peak assignments in the latter
spectrum were confirmed, where possible, through HMBC and HSQC experiments.
Scheme 1. Synthesis of the pyridinium salt 2.
O
O S
O
Cl-
N
OH
N
CH3
O2N
O2N
O2N
TsCl, Py
0 oC
N
H
N
H
N
H
1
1a
2
The synthesis of 2 presumably proceeds through the intermediate p-toluenesulfonate derivative 1a,
followed by nucleophilic displacement with pyridine [11] and then sulfonate/chloride exchange on the
addition of concentrated HCl in the reaction work up (Scheme 1). The nucleophilic displacement
would be expected to be facile at the benzylic site which is also activated through extended N-lone pair
electron delocalisation.
A single crystal X-ray study provided unequivocal structural confirmation for 2 including the
presence of the chloride counterion (Table 1; Figure 1a). The compound is ionic and a single formula
unit devoid of crystallographic symmetry comprises the asymmetric unit of the structure. The
determination is nicely precise with non-hydrogen geometries being summarized in Table 2. The
quaternary cation and its stereochemistry is depicted in Figure 1a, together with the associated chloride
ion. Interestingly, the pyridinium ring plane lies over that of the heterocyclic component of the indole,
C(2)…N(221) being only 2.930(2) Å (Figure 1b) possibly as a result of a favourable electronic
interaction between the electron deficient pyridinium moiety and the electron rich fused pyrrolo ring in
the indole; the other interatomic distances are more divergent with the two ring systems having an
interplanar dihedral angle of 17.91(4)°. The substituent pattern introduces some irregular features into
the C6 ring of the indole fragment: C(6)-C(7) is short (1.3749(15) Å) while C(3a)-C(7a) is long
(1.4217(14) Å) with the angles at the opposed C(5,7a) enlarged (124.14(10), 122.70(9)°) and those at

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Molecules 2011, 16
C(4,7) diminished (116.93(9), 117.69(9)°). At C(2) there is a gross asymmetry of ca. 10° in the
exocyclic angles, despite the twist of the pendant aromatic ring plane (Table 2). The angle sum at the
pyridinium nitrogen atom is 360.0°. The chloride ion has only one close contact: Cl...N,H(1)
3.0937(12), 2.28 Å (Cl…H(1)-N 154°), and is sufficiently close to the positive charge to be considered
associated with the quaternized pyridinium nitrogen atom (Figure 1a), so that it resides in the lattice as
an ion-pair. Crystal packing is dominated by inversion-related interactions between the planar residues,
and diverse interspecies hydrogen contacts to other nitro and chloride components.
Table 1. Crystal data for compound 2.
Formula
Fw
C20H16ClN3O2
365.8
Crystal system
Space group
a (Å)
b (Å)
c (Å)
Monoclinic
P21/c (#14)
10.274(3)
13.101(4)
13.439(4)
107.702(7)
1723.2(9)
1.410
β (°)
V (Å3)
Dc (g cm−3)
Z (f.u.)
4
2.4
μ (cm−1)
Specimen (mm3)
'T'min/max
0.48 × 0.32 × 0.27
0.92
Table 2. Non-hydrogen interatomic distances (Å) and angles (°) for compound 2.
Atoms
Parameter
Atoms
Parameter
Distances
N(1)-C(2)
C(2)-C(3)
C(3)-C(3a)
C(3a)-C(4)
C(3a)-C(7a)
C(4)-C(5)
C(5)-N(5)
C(5)-C(6)
C(6)-C(7)
C(7)-C(7a)
N(1)-C(7a)
C(2)-C(21)
C(5)-N(5)
N(5)-O(51)
N(5)-O(52)
1.3859(13)
1.3710(15)
1.4328(14)
1.3954(15)
1.4217(14)
1.3863(14)
1.4514(14)
1.4028(15)
1.3749(15)
1.3997(14)
1.3623(14)
1.4737(15)
1.4514(14)
1.2309(14)
1.2358(13)
C(21)-C(22)
C(21)-C(26)
C(22)-C(23)
C(23)-C(24)
C(24)-C(25)
C(25)-C(26)
C(22)-C(220)
C(220)-N(221)
N(221)-C(222)
N(221)-C(226)
C(222)-C(223)
C(223)-C(224)
C(224)-C(225)
C(225)-C(226)
1.4050(16)
1.3979(15)
1.3989(16)
1.388(2)
1.381(2)
1.391(2)
1.5108(16)
1.4898(14)
1.3487(14)
1.3478(14)
1.374(2)
1.388(2)
1.387(2)
1.380(2)

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Molecules 2011, 16
Table 2. Cont.
C(2)-C(21)-C(22)
Angles
C(2)-N(1)-C(7a)
108.95(9)
109.46(9)
120.41(9)
130.02(9)
107.05(9)
134.46(9)
106.38(9)
119.03(9)
116.93(9)
124.14(10)
118.52(9)
117.33(9)
119.35(9)
117.69(9)
129.17(9)
122.70(9)
108.11(9)
119.16(9)
118.41(10)
122.44(10)
121.53(10)
119.37(10)
119.10(10)
118.93(10)
123.79(9)
117.24(10)
121.32(11)
119.65(11)
119.91(11)
121.01(11)
114.44(9)
119.21(9)
119.58(9)
121.17(9)
120.53(11)
119.32(12)
119.41(12)
119.31(11)
120.26(11)
N(1)-C(2)-C(3)
N(1)-C(2)-C(21)
C(3)-C(2)-C(21)
C(2)-C(3)-C(3a)
C(3)-C(3a)-C(4)
C(3)-C(3a)-C(7a)
C(4)-C(3a)-C(7a)
C(3a)-C(4)-C(5)
C(4)-C(5)-C(6)
C(4)-C(5)-N(5)
C(6)-C(5)-N(5)
C(5)-C(6)-C(7)
C(6)-C(7)-C(7a)
C(7)-C(7a)-N(1)
C(7)-C(7a)-C(3a)
N(1)-C(7a)-C(3a)
C(5)-N(5)-O(51)
C(5)-N(5)-O(52)
O(51)-N(5)-O(52)
C(2)-C(21)-C(26)
C(22)-C(21)-C(26)
C(21)-C(22)-C(23)
C(21)-C(22)-C(220)
C(23)-C(22)-C(220)
C(22)-C(23)-C(24)
C(23)-C(24)-C(25)
C(24)-C(25)-C(26)
C(21)-C(26)-C(25)
C(22)-C(220)-N(221)
C(220)-N(221)-C(222)
C(220)-N(221)-C(226)
C(222)-N(221)-C(226)
N(221)-C(222)-C(223)
C(222)-C(223)-C(224)
C(223)-C(224)-C(225)
C(224)-C(225)-C(226)
N(221)-C(226)-C(225)
Torsion angles (atoms denoted by number only, N italicized)
1-2-21-22
2-21-22-220
−63.5(2)
1.0(2)
21-22-220-221
22-220-221-226
−45.6(2)
−53.3(1)
Figure 1. Projection of the ion-pair of the pyridinium chloride salt 2 (a) through and (b)
normal to the plane of the indole component, showing crystallographic numbering, and
50% probability amplitude displacement ellipsoids for the non-hydrogen atoms, with
hydrogen atoms having arbitrary radii of 0.1 Å. Crystallographic numbering used is shown.
(a)

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Molecules 2011, 16
Figure 1. Cont.
(b)
A preliminary investigation of the antibacterial properties of compound 2 indicated it had only
weak antibacterial activity against Staphylococcus aureus (K2361 strain overexpressing the NorA
pump) and low pump inhibitory activity with respect to the antibacterial berberine in this mutant strain.
In view of this weak activity, the synthesis of other related quaternary salt analogues was not pursued,
although such analogues should be readily accessible via the same general route.
3. Experimental
3.1. General
The reaction was monitored by thin-layer chromatography (TLC) on Merck Silica gel 60 F254 with a
thickness of 0.2 mm on an aluminium sheet, and the compounds were detected by examination under
ultraviolet light and by exposure to iodine vapour. High resolution electron impact (EI+) MS was run
using a VG Autospec spectrometer operating at 70 eV and a source temperature of 250 °C with PFK
1
reference. The H- and 13C-NMR were determined at 299.92 and 75.42 MHz, respectively, with a
Varian Unity-300 spectrometer. The melting point (mp) determination was recorded on a Reichert
melting point apparatus and is reported uncorrected.
3.2. Synthesis of 1-[2-(5-Nitro-1H-indol-2-yl)phenyl]methylpyridinium Chloride (2)
To a solution of indole alcohol 1 (283.3 mg, 1.05 mmol) in dry pyridine (3 mL) was added
p-toluenesulfonyl chloride (294.0 mg, 1.5 mmol) at 0 °C, and the mixture then stirred for 20 h. The
resulting yellow suspension was poured into a mixture of 32% HCl (1.5 mL) in crushed ice (5 g), then
filtered, and washed with H2O then Et2O. The yellow solid was dried to yield the indole pyridinium
salt 2 (217.1 mg, 65.8%). Recrystallization from MeOH and DCM afforded the salt 2 as yellow prisms
1
(44.3 mg), m.p. 231 °C (decomp.). H-NMR (CD3OD) δ 6.01 (s, 2H, CH2), 6.68 (s, 1H, H-3), 7.49
(br.d, J = 9 Hz, 1H, H-7), 7.58–7.64 (m, 4H, H-3', H-4', H-5', H-6' in the 2-aryl group), 7.82–7.87 (m,
2H, H-3'', H-5'' in the pyridine ring), 8.07 (dd, J = 9.1, 2.2 Hz, 1H, H-6), 8.40–8.50 (m, 1H, H-4''), 8.54
(dd, J = 2.2, 0.4 Hz, 1H, H-4), 8.60 (dd, J = 6.9, 1.2 Hz, 2H, H-2'', H-6''). 13C-NMR (CD3OD) δ 64.2

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Molecules 2011, 16
(CH2), 105.7 (C-3), 112.6 (C-7), 118.5 (C-6), 118.6 (C-4), 129.0 (C-3a), 129.1 (3C, ArCH), 131.1
(ArCH), 131.5 (ArCH), 132.1 (ArCH), 132.5 (ArCH), 133.1 (C-2), 134.1 (C-2´), 139.9 (C-7a), 141.1
(C-1´), 143.1 (C-5), 145.9 (ArCH), 147.1 (ArCH). HRMS (EI): m/z calcd for C20H16N3O2 [Quaternary
ion]: 330.1243; found: 330.1251.
3.3. X-ray Structure Determination
A full sphere of CCD area-detector diffractometer data was measured on a pale-yellow prism
(Bruker AXS instrument; ω-scans, 2θmax = 75°; monochromatic Mo Kα radiation, λ = 0.71073 Å; T ca.
150 K) yielding 34023 total reflections, these merging to 8384 unique after empirical/multiscan
absorption correction (proprietary software; Rint = 0.026), and used in the full matrix least squares
refinement, refining anisotropic displacement parameter forms for the non-hydrogen atoms, hydrogen
atom treatment following a riding model, 6118 with I > 2σ(I) being considered 'observed'. Reflection
weights were: (σ2(Fo2 ) + (0.0665P)2 + 0.482P)–1 (P = (Fo2 + 2Fc2 )/3). R1 was 0.048; wR2 0.13; S 1.03;
|Δρmax| 0.54 e Å–3. Neutral atom complex scattering factors were employed within the SHELXL 97
program [12]. Pertinent results are given in Tables 1 and 2, and Figure 1a and b.
4. Conclusions
The facile preparation of a novel indole-substituted benzylic pyridinium salt 2 is described and the
salt characterized spectroscopically and through single crystal X-ray diffraction methodology. The
solid state conformation of 2 indicated an interesting overlap of the pendant pyridinium ion and the
indolic 5-membered ring.
Acknowledgements
We wish to thank the University of Wollongong, The University of Western Australia, and
Srinakharinwirot University for supporting this work, and Kim Lewis and Mr. Anthony Ball
(Northeastern University, Boston, USA) for the antibacterial testing, and Glenn Kaatz for kindly
providing S. aureus K2361. The award of UPA and IPRS scholarships and an Australian Endeavour
Award to Siritron Samosorn is also gratefully acknowledged.
Supporting Information Available
CCDC-816104 contains the supplementary crystallographic data for this paper (excluding structure
factor amplitudes). These data can be obtained free of charge via www.ccdc.cam.ac.uk/
conts/retrieving.html (or from the CCDC, 12 Union Road, Cambridge CB2 1EZ, UK;
Fax: +44 1223336033; E-Mail:deposit@ccdc.cam.ac.uk).
Conflict of Interest
The authors declare no conflict of interest.

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Molecules 2011, 16
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