Crystal structure and spectroscopic elucidation of 3-phenylpyridinium hydrogensquarate

Article abstract of DOI:10.1016/j.saa.2009.10.008

The novel 3-phenylpyridinium hydrogensquarate (1) has been synthesized and its structure and properties are elucidated spectroscopically, thermally and structurally, using single crystal X-ray diffraction, linear-polarized solid-state IR-spectroscopy, UV-spectroscopy, TGA, DSC, DTA and ESI MS. Quantum chemical calculations were used to obtain the electronic structure, vibrational data and electronic spectrum. 3-Phenylpyridinium hydrogensquarate, crystallizes in the space group P-1 and the ions in the unit cell are joined into layers by intermolecular NH...O{double bond, long}C_(Sq) bonds with bond lengths of 2.625 and 2.626 A, respectively. Hydrogentartarates form dimers by strong O{double bond, long}COH...OCO interactions (2.499 A).

Full text of DOI:10.1016/j.saa.2009.10.008

Spectrochimica Acta Part A 75 (2010) 172–176
Contents lists available at ScienceDirect
Spectrochimica Acta Part A: Molecular and
Biomolecular Spectroscopy
journal homepage: www.elsevier.com/locate/saa
Crystal structure and spectroscopic elucidation of 3-phenylpyridinium
hydrogensquarate
Bojidarka B. Kolevaa,b,∗, Tsonko Kolevb, Tsanko Tsanevc, Stefan Kotovc,
Heike Mayer-Figgea, Michael Spitellerb, William S. Sheldricka
a Lehrstuhl für Analytische Chemie, Ruhr-Universität Bochum, Universitätsstraße 150, 44780 Bochum, Germany
b Institut für Umweltforschung, Universität Dortmund, Otto-Hahn-Strasse 6, 44221 Dortmund, Germany
c Burgas University, Faculty of Chemistry, 1, J. Bouchier, Blvd., 1164 Burgas, Bulgaria
a r t i c l e i n f o
a b s t r a c t
Article history:
The novel 3-phenylpyridinium hydrogensquarate (1) has been synthesized and its structure and proper-
ties are elucidated spectroscopically, thermally and structurally, using single crystal X-ray diffraction,
linear-polarized solid-state IR-spectroscopy, UV-spectroscopy, TGA, DSC, DTA and ESI MS. Quantum
chemical calculations were used to obtain the electronic structure, vibrational data and electronic spec-
trum. 3-Phenylpyridinium hydrogensquarate, crystallizes in the space group P−1 and the ions in the unit
cell are joined into layers by intermolecular NH· · ·O C(Sq) bonds with bond lengths of 2.625 and 2.626 Å,
respectively. Hydrogentartarates form dimers by strong O COH· · ·OCO interactions (2.499 Å).
© 2009 Elsevier B.V. All rights reserved.
Received 17 November 2008
Received in revised form
27 September 2009
Accepted 8 October 2009
Keywords:
3-Phenylpyridinium hydrogensquarate
Crystal structure
Solid-state linear polarized IR-spectroscopy
UV
Quantum chemical calculations
ESI MS
TGV
DSC
1. Introduction
For these reasons we have been performing a systematic study
of the effect of protonation on the structure and spectroscopic
The continuing interest in N-heterocyclic tertiary amines is a
result of their biological activity as for example, they can increase
the strength of the nerve signal [1]. These compounds exert their
action by inhibiting the voltage-dependent K-channels [2] and
hence maintain the presynaptic action potential. In this form the
calcium influx is enhanced, leading to an increase in the release
of neurotransmitter [3]. Due to their ability to facilitate nerve
transmission, aminopyridines have been applied to reverse anaes-
thesia and muscle relaxation [4]. In addition, they have been
proposed as drugs for the treatment of multiple sclerosis [5],
myasthenia gravis [6], spinal cord injuries [7], botulism [8] and
Alzheimer’s disease [9]. Pyridines are weak bases, pKa ∼ 9.0, and
thus they can exist as both the neutral or cationic protonated
form at physiological pH. This characteristic complicates the elu-
cidation of the mechanism and site of action [10]. Hypotheses
concerning the degradation pathways and chemical structure of
degradation products of aminopyridines have been presented [11].
properties of different substituted pyridines [12–17]. We now
present a spectroscopic and structural study of 3-phenylpyridinium
hydrogensquarate (1) (Scheme 1) both in solution and in the
solid state using the methods of single crystal X-ray diffraction,
ESI mass spectrometry, UV-spectroscopy, conventional and lin-
ear polarized IR-spectroscopy, and the TGV and DSC techniques.
Quantum chemical calculations at the DFT, MP2 and CIS levels
of theory and a 6-311++G** basis set were employed for predict-
ing and supporting experimentally observed optical properties of
the compounds studied. Independently of the above discussed 3-
phenylpyridine is used as a co-ligand in the “Second-Generation”
drugs development [18], and the crystallographic and spectro-
scopic investigations of this compound are rare. Only the crystal
structure of bis(aspirinato)-bis(3-phenylpyridine)-copper(II) has
previously been reported [18].
2. Experimental
2.1. Methods
∗
Corresponding author at: Lehrstuhl für Analytische Chemie, Ruhr-Universität
Bochum, Universitätsstraße 150, 44780 Bochum, Germany.
Tel.: +49 0231 755 79 69.
3-Phenylpyridine was purchased from Sigma–Aldrich (Ger-
many).
E-mail address: B.Koleva@infu.tu-dortmund.de (B.B. Koleva).
1386-1425/$ – see front matter © 2009 Elsevier B.V. All rights reserved.
doi:10.1016/j.saa.2009.10.008

B.B. Koleva et al. / Spectrochimica Acta Part A 75 (2010) 172–176
173
the KBr disk technique. The oriented samples were obtained as a
colloid suspension in a nematic liquid crystal ZLI 1695. The the-
oretical approach, and the experimental technique for preparing
the samples as well as procedures for polarized IR-spectra inter-
pretation and the validation of this new linear-dichroic infrared
(IR-LD) orientation solid-state method for accuracy and precision
have been presented. The influence of the liquid crystal medium
on peak positions and integral absorbances of the guest molecule
bands, the reological model, the nature and balance of the forces in
the nematic liquid crystal suspension system, and the morphology
of the suspended particles have also been discussed [21–24].
The positive and negative ESI mass spectra were recorded on a
Fisons VG Autospec instrument employing 3-nitrobenzylalcohol
(Sigma–Aldrich) as the matrix.
Ultraviolet (UV) spectra were recorded on Tecan Safire
Absorbance/Fluorescence XFluor 4 V 4.40 spectrophotometer oper-
ating between 190 and 900 nm, using ethanol solvent (Uvasol,
Merck product) in concentration of 2.5 × 10−5 M, using 0.921 cm
quartz cells.
Quantum chemical calculations are performed with GAUSSIAN
98 and Dalton 2.0 program packages [25,26]. The output files are
visualized by means of the ChemCraft program [27]. The geome-
try of protonated form of 3-phenylpyridine was optimized at two
levels of theory: second-order Moller-Pleset perturbation theory
(MP2) and density functional theory (DFT) using the 6-311++G**
Scheme 1. Chemical diagram of (1).
The X-ray diffraction intensities were measured in the ␻ scan
mode on a Siemens P4 diffractometer equipped with Mo K␣ radi-
ation (ꢀ = 0.71073 Å, ꢁmax = 25◦) and the structure was solved by
direct methods and refined against F2 [19,20]. An ORTEP plot illus-
trates the anion and cation structures at the 50% probability level.
Relevant crystallographic structure data and refinement details are
presented in Table 1, selected bond distances and angles in Table 2.
The hydrogen atoms were constrained to calculated positions and
refined using riding models in all cases.
Conventional and polarized IR-spectra were measured on
a Thermo Nicolet OMNIC FTIR-spectrometer (4000–400 cm−1
,
2 cm−1 resolution, 200 scans) equipped with a Specac wire-grid
polarizer. Non-polarized solid-state IR spectra were recorded using
Table 1
Crystal and refinement data for (1).
Empirical formula
Formula weight
Temperature (K)
C15H11NO4
269.25
294(2)
0.71073
Wavelength (Å)
Crystal system, space group
Unit cell dimensions
Triclinic, P−1
a = 6.4559(18) Å
b = 7.558(3) Å
c = 13.289(5) Å
634.2(4)
˛ = 88.96(3)◦
ˇ = 87.86(3)◦
ꢂ = 78.19(3)◦
Volume (Å3)
Z
2
Calculated density (mg m−3
Absorption coefficient (mm−1
F(0 0 0)
)
1.410
0.104
280
)
Crystal size (mm)
ꢁ range for data collection
Limiting indices
Reflections collected/unique
Absorption correction
Goodness-of-fit on F2
Final R indices [I > 2ꢃ (I)]
R indices (all data)
0.30 × 0.31 × 0.45
3.14 ≤ ꢁ ≤ 24.99
−1 ≤ h ≤ 7, −8 ≤ k ≤ 8, −15 ≤ l ≤ 15
1915/1703, R(int) = 0.0468
scans
1.532
R1 = 0.0557, wR2 = 0.1754
R1 = 0.0636, wR2 = 0.1821
Table 2
Selected bond lengths [Å] and angles [◦] for (1) from crystallographic data.
O14 C14 1.249(4)
O13 C13 1.246(4)
O12 C12 1.224(3)
O15 C15 1.312(3)
C15 C14 1.411(5)
C15 C13 1.435(4)
C15 C12 2.041(4)
C13 C12 1.479(5)
N1 C4 1.342(3)
N1 C1 1.336(4)
C9 C11 1.384(3)
C9 C8 1.383(4)
C10 C2 1.383(3)
C10 C6 1.401(4)
C8 C7 1.396(5)
C8 C6 1.489(3)
C11 C3 1.385(5)
C7 C5 1.386(3)
C6 C4 1.370(4)
C5 C3 1.366(5)
C2 C1 1.355(5)
C14 C12 1.484(4)
O15 C15 C14 131.0(3)
O15 C15 C13 135.9(3)
C14 C15 C13 93.1(2)
O15 C15 C12 177.6(3)
C14 C15 C12 46.66(17)
C13 C15 C12 46.41(19)
O14 C14 C15 136.1(2)
O14 C14 C12 134.3(3)
C15 C14 C12 89.6(3)
O13 C13 C15 136.7(3)
O13 C13 C12 134.4(2)
C15 C13 C12 88.9(3)
O12 C12 C13 137.0(3)
O12 C12 C14 134.6(3)
C13 C12 C14 88.4(2)
O12 C12 C15 178.3(3)
C13 C12 C15 44.65(16)
C14 C12 C15 43.72(18)
C4 N1 C1 122.6(3)
C11 C9 C8 120.6(3)
C2 C10 C6 120.8(3)
C9 C8 C7 119.0(3)
C7 C8 C6 120.5(3)
C3 C11 C9 119.8(3)
C5 C7 C8 119.9(3)
C4 C6 C10 117.0(2)
C4 C6 C8 122.2(3)
C10 C6 C8 120.8(3)
C3 C5 C7 120.5(3)
N1 C4 C6 120.7(3)
C5 C3 C11 120.1(3)
C1 C2 C10 119.2(3)
N1 C1 C2 119.7(2)
C9 C8 C6 120.5(3)

174
B.B. Koleva et al. / Spectrochimica Acta Part A 75 (2010) 172–176
basis set. The DFT method employed is B3LYP, which combines
Backe’s three-parameter non-local exchange function with the cor-
relation function of Lee, Yang and Parr. Molecular geometries of
the studied species were fully optimized by the force gradient
method using Bernys’ algorithm. For every structure the station-
ary points found on the molecule potential energy hypersurfaces
were characterized using standard analytical harmonic vibrational
analysis. The absence of the imaginary frequencies, as well as of
negative eigenvalues of the second-derivative matrix, confirmed
that the stationary points correspond to minima of the potential
energy hypersurfaces. The calculation of vibrational frequencies
and infrared intensities were checked to establish which kind of
performed calculations agree best with the experimental data. In
our cases the DFT method provides more accurate vibrational data,
as far as the calculated standard deviations of respectively 7 cm−1
(B3LYP) and 12 cm−1 (MP2) corresponding to groups which do
not participate in intra- or intermolecular are concerned. So, the
MP2/6-311++G** data are presented for above discussed modes,
where a modification of the results using the empirical scaling fac-
tor 0.8929 is made to achieve better correspondence between the
experimental and theoretical values. The UV spectra of (1) in the
gas phase and in ethanol solution are obtained by CIS/6-311++G**
and TDDFT calculations.
Fig. 1. The molecular structure of (1), showing the atom-labeling scheme. Displace-
ment ellipsoids are drawn at the 50% probability level.
Fig. 2. Linkage of the molecules into layers and the unit cell of (1).
The thermal analyses were performed in the 300–500 K region
on a Differential Scanning Calorimeter PerkinElmer DSC-7, and a
Differential Thermal Analyzer DTA/TG (Seiko Instrument, model
TG/DTA 300). The experiments were carried out with scanning rate
of 10 K/min under an argon atmosphere.
joined into layers (Fig. 2) by intermolecular NH· · ·O C(Sq) bonds
(2.625 and 2.626 Å). The hydrogentartarate anions form dimers, a
structural motif typical for systems with pyridinium counterions
[16], by strong intermolecular O COH· · ·OCO interactions with a
length of 2.625 Å. The unit cell contains two cations with a mutu-
ally co-planar orientation of the pyridine and phenyl rings, thus
indicating a co-linear orientation of the corresponding out-of-plane
modes of both aromatic systems (Fig. 2). The pyridine and phenyl
planes are tilted towards one another in the individual cations and
exhibit an interplanar angle of 38.0(2)◦. The transition moments of
the ꢄNH functions are co-linear and the resulted moment adopt a
direction, coinciding with that of the N–H bond (Fig. 2).
The elemental analysis was carried out according to the standard
procedures for C and H (as CO2, and H2O).
2.2. Synthesis
3-Phenylpyridinium hydrogensquarate (1) was synthesized by
the following way: 0.1130 g squaric acid was added to 5 ml of 3-
phenylpyridine withcontinuousstirringand heatingat 80 ◦Cfor5 h.
A colourless polycrystalline sample was obtained from the result-
ing solution after 5 days. The product was filtered off and dried
under air. Single colourless crystals, suitable for X-ray analyses,
were grown from a methanol–water (1:1) solution at room temper-
atureover aperiod of aweek. (Found: C, 66.90;H, 4.10;[C15H11NO4]
calcd.: C, 66.91; H, 4.12%.) The most intensive signal in the positive
ESI mass spectrum is that of the peak at m/z 156.77, corresponding
to the singly charged cation [C11H10N]+ with a molecular weight of
156.21. The TGV and DSC data in temperature range of 300–500 K
show an absence of included solvent molecules in (1).
The MP2/6-31++G** level of approximation leads to an
optimization of the structure of protonated 3-phenylpyridine
correlating well with the experimental geometrical parameters
(compare Table 2 with Scheme 2). Differences between theoreti-
cal and experimental values of less than 0.0333 Å and 3.4(4)◦ are
obtained. The pyridine and benzene planes are tilted off at an angle
of 34.5(3)◦, thereby showing a difference of 3.4(4)◦ compared with
corresponding experimental value.
3.2. Theoretical and experimental IR-spectroscopic data
3. Results and discussion
The hydrogensquarates are usually characterized by broad and
strongly overlapped IR-spectroscopic patterns [28]. For this rea-
son our experimental IR-spectroscopic elucidation is supported
by theoretical quantum chemical calculations of the vibrational
properties of the counterion. The vibrational analysis of the hydro-
gensquarate anion has been presented in [29].
3.1. Crystal structure of (1) and molecular geometry of
protonated 3-phenylpyridine
3-Phenylpyridinium hydrogensquarate, crystallizes in the cen-
trosymmetric space group P−1 (Fig. 1). The molecules of (1) are
Scheme 2. Geometry parameters of protonated 3-phenylpyridine at the MP2/6-31++G** level of approximation.

B.B. Koleva et al. / Spectrochimica Acta Part A 75 (2010) 172–176
175
Fig. 4. Solid-state IR-spectrum of (1) in KBr pellet; (A) non-polarized IR-(1) and
Fig. 3. Theoretical IR-spectrum of protonated 3-phenylpyridine and illustration of
some transition moments of protonated 3-phenylpyridine. The corresponding fre-
quencies are given in [cm−1].
reduced IR-LD (2) spectra of (1) in a nematic host after elimination of the band at
676 cm−1
.
sponds to i.p. stretching vibrations of aromatic fragments. The
ꢄN+H and ꢄOH bands are strongly overlapped and are observed
within the 3000–1900 cm−1 region. The well defined bands at
The calculated IR-spectrum of protonated 3-phenylpyridine is
depicted in Fig. 3. Selected transition moment directions, impor-
tant for experimental IR-LD analysis are visualized in Scheme 3.
The IR-band at 3568 cm−1 belongs to the ꢄN+H stretching vibration,
while the corresponding ıN+H bending mode can be assigned to
the band at 1670 cm−1. The series of in-plane vibrations of both
the pyridine and phenyl rings are observed within the 3100–3000
and 1653–1502 cm−1 ranges. The out-of-plane (o.p.) bending vibra-
tions of the aromatic rings are obtained within 1000–400 cm−1
(956 (ph), 877 (py), 827 (py), 767 (ph), 746 (ph + py), 725 (ph),
705 (py), 422 (ph) and 413 cm−1 (py), respectively). Selected tran-
sition moments are visualized in Fig. 3. The calculated IR-bands
are typical for aromatic pyridine and phenyl rings. In contrast to
some substituted pyridines [13–15], where the Npy-protonation
leads to a partial charge redistribution or stabilizing of the quinoide
form, practically all the IR-characteristic bands are only weakly
affected in 3-phenylpyridine. This conclusion is supported by the
obtained single charge redistribution of the protonated molecule,
where Scheme 3 shows that the positive charge is localized at the
1798 and 1662 cm−1 belong to ꢄs O and ꢄC C stretching vibrations
C
of the hydrogensquarate anion (Sq). The corresponding ꢄas
C
O(Sq)
and ıN+H bands are strongly overlapped and practically cannot
be define precisely by conventional IR-techniques. The bands at
820, 767 and 746 cm−1 belong to o.p. of pyridine and benzene
rings. The strong overlapping causes difficulties in the applica-
tion of the reducing-difference procedure for interpretation of the
polarized IR-LD spectra within 3100–850 cm−1 region. Success-
ful employment of the method is used only for the bands within
850–400 cm−1. As can be seen in Fig. 4A the simultaneously elim-
ination of the bands at 693 and 676 cm−1 at an equal dichroic
ratio confirms their origin as in-plane vibrations of the aromatic
fragments (the theoretical values are at 690 and 675 cm−1, respec-
tively).
3.3. Electronic spectra
protonated atom Npy
.
The UV-spectrum of (1) in ethanol is depicted in Fig. 5. The
observed bands at 240 and 252 nm with e values of 1023 and
1783 l mol−1 cm−1 belong to B-bands of both the phenyl and pyri-
dine fragments. TD-DFT calculations in ethanol solution give a
The experimental IR-spectrum of (1) in solid-state is depicted
in Fig. 4. The bands within the 3100–3000 cm−1 range corre-
Scheme 3. Single charge distribution in protonated 3-phenylpyridine.
Fig. 5. UV-spectrum of (1) in ethanol.

176
B.B. Koleva et al. / Spectrochimica Acta Part A 75 (2010) 172–176
good correlation with the experimental data (240 nm (F = 0.0015)
and 250 nm (F = 0.091)). These data clearly indicate that the Npy
protonation only weakly affects on the aromatic character of the
3-phenylpyridine molecule [13,15].
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B.K. wishes to thank the Alexander von Humboldt Foundation
for a Fellowship. T.K. and M.S. thank DAAD for a grant within the
priority program “Stability Pact South-Eastern Europe” and the DFG
for project SP 255/21-1.
Appendix A. Supplementary data
Supplementary data associated with this article can be found, in
the online version, at doi:10.1016/j.saa.2009.10.008.
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